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产品编号 BC00024
名称 CLUSTAL W
类别 Alignment Search software
简介 Multiple sequence alignment. It
is a complete overhaul and upgrade of CLUSTAL V
品编号 BC00028
名称 DFBLAST
类别 Alignment Search software
简介 Module to read a BLAST output and
to generate an annotated query.
产品编号 BC00034
名称 FSAP
类别 Alignment Search software
简介 Rapid Sequence Comparison
产品编号 BC00035
名称 GAP
类别 Alignment Search software
简介 A Global Alignment Program
产品编号 BC00041
名称 LAV
类别 Alignment Search software lav
and related tools is an application that
provides a way to display and browse through
the sequence alignments computed by a variety
of programs.(sim , blast ...)
产品编号 BC00043
名称 LFASTA
类别 Alignment Search software
简介 local similarity searches showing
local alignments.The algorithm used to
calculate the local alignment in a band has
been improved
产品编号 BC00045
名称 MACAW
类别 Alignment Search software
简介 Multiple Alignment Construction & Analysis
Workbench MACAW is a program for locating,
analyzing, and editing blocks of localized
sequence similarity among multiple seqences
and linking them into a composite multiple
alignment.
产品编号 BC00048
名称 MBLKP and MBLKN
类别 Alignment Search software
简介 Utilities for Finding Local Multiple Similarities.
Two utilities are provided to perform a search for
blocks of local similarity along multiple protein
(mblkp) and nucleic acid (mblkn) sequences using the
MACAW search algorithm (Schuler, et al., 1991).
Unlike MACAW, which requires Microsoft Windows
graphical interface, these simple utilities are
designed as console-style programs, and as such,
may be compiled for execution on a wide variety of
platform. Note that without a graphical interface,
much of the functionality of the MACAW program cannot
be included. In particular, it is not possible to link
the blocks together to form a composite multiple alignment.
产品编号 BC00049
名称 MEMFILE
类别 Alignment Search software
简介 Memfile is part of blast package
Basic Local Alignment Search Tool
family of sequence database comparison
programs manage the loading, updating, and
dropping of files mapped into shared memory
segments.
产品编号 BC00054
名称 PLALIGN
类别 Alignment Search software
简介 a version of lalign that plots the local
alignments to a screen or to a Tektronix
terminal emulator.
The PLALIGN program incorporate the de "sim"
algorithm described by Huang and Miller
Adv. Appl. Math. 12:337-357(1991).
产品编号 BC00055
名称 PLFASTA - PCLFASTA
类别 Alignment Search software
简介 PLFASTA : local similarity searches with plot
output (on the IBM, this program requires
that the environment variable BGIDIR be
set).PCLFASTA(unix only) local similarity
searches with plot output using pic commands.
产品编号 BC00057
名称 PRDF
类别 Alignment Search software
简介 a version of RDF2 that uses calculates the probability of
a
similarity score more accurately by using a fit to an extreme
value distribution. Code to fit the extreme value distribution
parameters and the impetus to update RDF2 was provided by Phil
Green, Washington U., St.Louis.
产品编号 BC00059
名称 PRSS
类别 Alignment Search software
简介 a version of PRDF that uses a rigorous Smith-Waterman
calculation to score similarities
作者 William Pearson
产品编号 BC00061
名称 ROBUST
类别 Alignment Search software
简介 locating well-conserved regions within a
pairwise alignment.
产品编号 BC00062
名称 RSS
类别 Alignment Search software
简介 a version of RDF2 that uses a rigorous Smith-
Waterman calculation to score similarities
The RSS program incorporate algorithms
described by Huang, Hardison, and Miller
Comput. Appl. Biosci. 6:373-381(1990).
产品编号 BC00070
名称 TBLASTN
类别 Alignment Search software
简介 Basic Local Alignment Search Tool
family of sequence database comparison
programs tblastn: compare an amino acid query
sequence against a nucleotide sequence
database translated in all 6 reading frames.
产品编号 BC00071
名称 TDALIGN
类别 Alignment Search software
简介 -
产品编号 BC00072
名称 TFASTA
类别 Alignment Search software
简介 Search DNA library for a protein sequence by
translating the DNA sequence to protein
in all six frames(three forward frames with
the -3 command line option).TFASTA with ktup=2
is about as fast as a DNA FASTA with ktup=4,
and is substantially more sensitive.
产品编号 BC00083
名称 ALSCRIPT
类别 Alignment editing and display
简介 Program to take a multiple protein sequence alignment
and "prettify" it. Boxing, shading, font changes etc.
产品编号 BC00103
名称 PROSET
类别 Database and analysis
简介 program to create non-redundant
sets of protein sequences
产品编号 BC00110
名称 Linkage Analysis Package
类别 Genetic Linkage software
简介 The Linkage Analysis Package (LINKAGE) is an integrated system
of programs designed to perform linkage analysis and genetic
risk calculations.
产品编号 BC00116
名称 GAS
类别 Genetic tools
简介 This package provides facilities for reading, writing,
sectioning and performing statistical analyses on
phenotypic and genotypic data.
产品编号 BC00123
名称 BABEL
类别 Molecular modelling and graphics
简介 file conversion
Input_Format: Mopac Cartesian Mopac Internal Mopac Output
Input_Format: CSD GSTAT CSD CSSR Free Form Fractional
Input_Format: Macromodel MM2 Output PDB
Input_Format: Alchemy XYZ Mac Molecule
Input_Format: Chem3D MicroWorld Ball and Stick
Input_Format: MOLIN
Output_Format: Mopac Cartesian Mopac Internal Gaussian Input
Output_Format: IDATM Macromodel Mac Molecule
Output_Format: MM2 Input MM2 Ouput PDB file
Output_Format: Report of interatiomic distances,angles,and torsions
Output_Format: Alchemy XYZ Ball and Stick
Output_Format: Chem3D MicroWorld
产品编号 BC00132
名称 MSP
类别 Molecular modelling and graphics
简介 "MSP" (Molecular Surface Package) can be licensed
(Academic
pricing). The package will render vertices, edges, and triangles
of a molecular surface polyhedron; pixel map of RGB values for
a
rendered surface and model; calculate contact, reentrant, molecular,
and accessible area of each atom;and list cavities:centroid,
volume,
area, and bordering atoms. It has lots of other capabilities
as well.
产品编号 BC00136
名称 CEPH
类别 Genome Mapping Databases
简介 The Centre d'Etude du Polymorphisme Humain (CEPH) maintains
a
database of genotypes for all genetic markers that have been
tested in the reference families for linkage mapping of the
human chromosomes.
产品编号 BC00146
名称 SCHAKAL
类别 Molecular modelling and graphics
简介 molecules, crystal sections + surfaces
"realistic" shading incl. highlights + shadows
(depth dependent) lightness + pseudo-transparency
automatic labelling of atoms, broken bonds
Input_Format: atom names + coordinates, (symmetry), SHELX
Output_Format: atom names + coordinates
Molecular_Model: wire, ball_and_stick, CPK
Output_Type: 8 bit (256 colours) display, HPGL, HP L.Jet III
产品编号 BC00149
名称 Squid
类别 Molecular modelling and graphics
简介 simple_molecule, drug, polymer, protein, inorganic, DNA,
XY-plot
XYZ-plot, Data-processing, Crystallographic Analysis, MD analysis
Cluster analysis,
Input_Format: PDB, KARPLUS, GROMOS, AMBER, General Ascii files
Output_Format: PDB, KARPLUS, MD-trajectory, General Ascii files
Molecular_Model: wire, stick, stick_and_ball, CPK, ribbon,
Molecular_Model: alpha_trace, colour, stereo, vectors, labels
Output_Type: display, PostScript, HPGL, Xfig, (plot84), user
产品编号 BC00155
名称 OSP
类别 Oligomer design and synthesis
简介 OSP is a computer program developed to aid in
selecting oligonucleotide primers for DNA
sequencing and for the polymerase chain
reaction. OSP allows the user to specify (or
use default) constraints for primer and
amplified product lengths, %G+C contents,
and (absolute or relative) meltingtemperatures
for primer 3' nucleotides; and for the maximum
allowable primer-self,primer-primer, and
primer-product annealing propensities.
Candidate primer sequences are screened
against a user-supplied data set of other
sequences (e.g. repetitive element or vector
sequences) to help minimize the possibility of
non-specific priming.
Primers meeting all constraints are ranked and
displayed in order of increasing overall
``score'', which is a user-definable weighted
sum of the above parameter values.
The program is available at no cost from the
authors in two versions, one of which produces
text-only output, and the other having an
interactive X windows graphic interface.
产品编号 BC00158
名称 PRIMER - MIT
类别 Oligomer design and synthesis
简介 PRIMER is a computer program for selecting PCR primer pairs
to
amplify specific regions of sequenced DNA. While PRIMER was
specifically designed to select primers from cloned and
sequenced genomic DNAs, many of the tests it performs are useful
for selecting oligos for other types of experiments as well,
including other PCR applications, oligo hybridization and
dideoxy sequencing.
There are two versions of this program : primer.0.5 and Primer2.2
产品编号 BC00171
名称 PHYLIP
类别 Phylogeny
简介 free package of programs for inferring
phylogenies,including programs to carry
out parsimony, compatibility, distance matrix,
invariants ("evolutionary parsimony") and
likelihood methods on a variety of
different kinds of data.
产品编号 BC00176
名称 ANTHEPROT
类别 Protein sequence analysis
类别 Protein structure analysis
类别 Structure prediction
类别 Pattern Identification
类别 Alignment Search software
类别 Alignment editing and display
类别 Alignment browser
类别 Molecular modelling and graphics
简介 ANalyze THE PROTeins
ANTHEPROT is a package that allow to make:
* Study of physico-chemical properties: hydrophobicity,
antigenicity, flexibility, solvent accessibility,
amphiphilicity.
* Secondary structure prediction: Chou & Fasman, Garnier,
Gibrat, Deleage, Levin.
* Prediction of transmembranous regions & of structural
domains.
* Multiple alignment : Method of Feng & Doolittle, Higgins,
Needleman & Wunsch.
* Search for biological sites using PROSITE, and PATMAT
from J.C. Wallace & S.Henikoff.
* Search for homologous protein : Program FASTA (W. Pearson)
* Identity level between several sequences.
* Look and handle protein structures from PDB
* Tools: Editor, File, Printing, format, colors ...
产品编号 BC00178
名称 GREASE
类别 Protein sequence analysis
Kyte-Doolittle hydropathicity profile
产品编号 BC00182
名称 RELATE
类别 Protein sequence analysis
简介 significance program described by Dayhoff
(Atlas of Protein Sequence and Structure,
Vol. 5, Supplement 3).Each chunk of 25 residues
in one sequence is compared to every 25
residue fragment of the second sequence.
Sequences which are genuinely related will
have a large number of scores greater than
3 standard deviations above the mean score of
all of the comparis
产品编号 BC00185
名称 TGREASE
类别 Protein sequence analysis
简介 graphic plot of Kyte-Doolittle profile
产品编号 BC00193
名称 MEMSAT
类别 Protein structure analysis
简介 MEMbrane protein Structure And Topology
产品编号 BC00206
名称 RESTMAP
类别 Restriction maps
简介 Restriction mapping programs MAPC (circular mo-
lecules) and MAPL(linear molecules)
In addition, an improved data entry program
DIGED, is included.
产品编号 BC00209
名称 ENTREZ
类别 Searching databases
简介 Entrez is a molecular sequence retrieval
system developed at the National Center for
Biotechnology Information (NCBI)
Entrez provides an integrated approach for
gaining access to nucleotide and protein
sequence information, to the MEDLINE citations
in which the sequences were published, and to
a sequence-associated subset of MEDLINE. The
sequence records are derived from a variety of
database sources, including GenBank, EMBL,
DDBJ, PIR, SWISS-PROT, PRF, and PDB. With
Entrez and a personal computer, you can rapidly
search several hundred megabytes of sequence
and literature data using techniques that are
fast and intuitive. The retrieval software and
associated databases are distributed on CD-
ROMs, but may be mounted on a file server and
installed on multiple computers on a local
network if desired.
The /entrez/current directory of the NCBI
anonymous ftp server is used for updates to
the Entrez executables for a given release of
the Entrez: Sequences and Entrez: References
CD-ROMs. The Entrez application requires that
you obtain the NCBI Entrez CD-ROMs.To request
subscription information on Entrez, please
send an email message to info@ncbi.nlm.nih.gov.
Include your full postal address and your phone
and fax numbers.
产品编号 BC00218
名称 BIGPROBE
类别 Sequence analysis
产品编号 BC00223
名称 DM5
类别 Sequence analysis
产品编号 BC00224
名称 DNA WorkBench
类别 Sequence analysis
简介 A program for sequence searching and manipulation
Powerful and fast searches on Genbank and other databases.
Client-server: access remote databases and programs
Parallel distributed processing for huge databases of the near
future.
Many sequence manipulation functions.
This list keeps growing. At present, it includes calculating
the reverse complement, displaying reading frames and nucleotide
to protein translations, editing, searching for restriction
enzyme sites, searching for human repeat or vector in a sequence,
comparing a sequence against a library or a user file, searching
for a regular expression in a sequence.
On my to-do list: contig assembly, searching by context-free
and other grammars, feature table manipulation, GDB access,
approximate regular expression matching, physical mapping of
chromosomes, ...
产品编号 BC00239
名称 GENINFO SOFTWARE TOOLBOX
类别 Sequence analysis
简介 The GenInfo Software Toolbox is a set of
software and data exchange specifications that
are used by NCBI to produce portable, modular
software for molecular biology.
api Application Programmer Interface,
Sequence Utilities
asn ASN.1 specifications for publications
and sequences asnlib Source code for AsnLib and
asntool asnload AsnLib headers and dynamic
parse tables (Mac and PC)
asnstat AsnLib headers that use static memory
(UNIX and VMS)
bin Asntool executable copied here
browser Source code for Entrez application
build Empty directory for building tools
and libraries
cdromlib Access routines for data on the
Entrez CD-ROM
cdrom06 Files for compatibility with Entrez
pre-release 6
config Configuration files for NCBI software
corelib Source code for NCBI Core Software
Library
data Data files used for sequence
conversion
demo AsnLib and sequence utility
demonstration programs
doc Documentation in ASCII files
include Include files required by
applications are copied here
lib Libraries copied here
macmpw Files for compiling with Macintosh MPWC
make Make files for various systems
msdos Files for compiling with Microsoft C
for DOS
mswin Files for compiling with Microsoft C
and Windows
object Functions for reading and writing
complex objects
readme File that contains important building
instructions
vibrant Source code for Vibrant portable
interface package
产品编号 BC00247
名称 NCBI
类别 Sequence analysis
General purpose routines used by BLAST
产品编号 BC00267
名称 MOLWT
类别 Chemistry
简介 There are already some excellent chemical calculation programs,
including CHEMCALC. MOLWT is not as versatile as these, but
it is much faster for what it does do, and it needs only 50
KB of
disk space (half of which is documentation). It will run on
any
DOS-based computer. Color is used for emphasis, but the screens
are legible on any kind of monitor.
产品编号 BC00270
名称 FROMGB
类别 Sequence format conversion tools
简介 convert from GenBank LOCUS format (also
used by the IBI-Pustell programs) to Pearson/
FASTA format.
产品编号 BC00284
名称 RDF2
类别 Statistical significance
简介 improved version of RDF program with all
three scoring methods (now includes local,
or window, shuffle routine)
产品编号 BC00287
名称 GARNIER
类别 Structure prediction
简介 A secondary structure prediction program
using the method of Garnier, Osgusthorpe,
and Robson, J. Mol. Biol. 120:97-120(1978).
产品编号 BC00293
名称 AUTOREADER
类别 -
产品编号 BC00334
名称 EMBL Network File Server
类别 e-mail Server RETRIEVAL
SERVER netserv@embl-heidelberg.de
简介 This server allows the retrieval via email of
EMBL and SWISS-PROT entries as well as a wide
variety of databases. It also allows the
retrieval of public domain software for MS-DOS
computers, the Apple Macintosh,DEC ,VAX/VMS,
and UNIX. The programs are distributed in
a form that is first compressed and then
converted from binary to a printable ASCII
text file.
Note : You can also obtain all of these
databases and software by FTP.If you have
access to FTP you should use that method
rather than use the email file server.
产品编号 BC00336
名称 GENE-SERVER e-mail Server
类别 e-mail Server RETRIEVAL
SERVER gene-server@bchs.uh.edu
简介 Allows to retrieve entries from the GenBank and PIR sequence
databases using various text search parameters. It also allows
the retrieval of public domain software for MS-DOS computers,
the Apple Macintosh, DEC VAX/VMS, and UNIX as well as additional
text files such as the BIO-Matrix newsletters.
产品编号 BC00346
名称 TOPS
类别 Protein structure analysis
简介 Program to automatically generate and edit protein
topology cartoons. These cartoons are two dimensional
representations of the secondary structure of proteins,
where helices are represented by circles and strands
by triangles. TOPS is made of two parts: Tops, the main
ansi C program and Xtops, an X windows topology cartoon
editor.
产品编号 BC00349
名称 PATTERN
类别 Pattern Identification
简介 Part of the ANTHEPROT software package for protein sequence
analysis. Can scan a sequence with the patterns stored in the
PROSITE.DAT file or with user-defind patterns stored using the
same syntax. The user can set an optional similarity thresold
or mismatch number.
产品编号 BC00350
名称 CREGEX
类别 Pattern Identification
简介 CREGEX reformats the native PROSITE database into a file
containing regular expressions, which can be used in the
pattern matching language AWK. Entries containing a range
are split into multiple patterns. The regular expression
file is most conveniently used in combination with
PROSEARCH scripts.
产品编号 BC00353
名称 Motif Master
类别 Pattern Identification
简介 Motif Master searches protein sequence files or sequence
databases against the PROSITE database. Files & databases
may
also be searched against user-generated databases or patterns.
Search results (pattern matches) may be displayed on-screen
or outputted to a file. Motif Master also searches the PROSITE
documentation file, from which specific chapters may be
retrieved. The program accepts DNA or RNA pattern databases
as
well, for searching nucleic acid sequence files. PIR, SWISS-
PROT, EMBL and GenBank formats are all compatible with Motif
Master.
产品编号 BC00354
名称 PATMAT
类别 Pattern Identification
类别 Searching databases
简介 General database searching tool with a simple and clear user
interface. Can searches PROSITE.DAT as a pattern database.
Searches other databases with patterns as probes.
产品编号 BC00360
名称 PROTOMAT
类别 Pattern Identification
简介 Reads an entry from PROSITE.DAT and extracts all true positive
and false negative sequences listed there from SWISS-PROT.
Runs H.O. Smith's "motif" algorithm (PNAS 87:826-830)
on the
group of proteins and extends the motifs into blocks.
Assembles a "best path" set of blocks describing the
group of
proteins.
产品编号 BC00363
名称 Random Cladistics
类别 Phylogeny
简介 With it you can bootstrap/jackknife/PTP/generate random tree
histograms and calculate confidence values on cladistic
coevolutionary questions. It is a package that includes the
following programs :
PTP.EXE, HEYJOE.EXE, TREES.EXE, LANYON.EXE, DANRAN.EXE,
RND.EXE, CHKLAN.EXE
产品编号 BC00378
名称 Rnadraw
类别 RNA analysis
简介 Rnadraw offers RNA optimal structure /
basepair-probability matrix / heat curve calculation on Intel
x86
compatible computers, providing a consistent user interface
with many possibilities to view, print, import/export and edit
calculation results.
产品编号 BC00384
名称 PROANAL
类别 Protein structure analysis
简介 ProAnal isfor analysis of the structure-activity relationship
in
a family of evolutionarily related (and/or artificially mutated)
proteins/peptides. The program uses aligned amino acid
sequences with data of their activity (pK, Km, ED50 or any
other) and searches for correlations between data on activity
and various physico-chemical characteristics of different
regions in primary structures. In automatic mode, the program
generates and verifies hypotheses on the disposition of a
sequential modulating region in a protein, and key
characteristics of the region. In manual mode, users can
generate and analyze their own hypotheses. The program is
implemented on IBM PC or compatible computers. It is designed
to
be easily handled by the occasional computer user and yet it
is
powerful enough for experienced professionals. Pro__Anal
operation is demonstrated on the example of finding modulating
centers in a family of disintegrins-proteins from snake venoms
which inhibit fibrinogen interaction with platelet receptors.
In
another example it is shown that the immunogenicity of peptides
is connected with their positive charge.
产品编号 BC00389
名称 RNA_d2
类别 RNA analysis
简介 RNA_d2 is a user-friendly program developped for interactively
generating aesthetic and non-overlapping drawings of RNA
secondary structures. It allows easy untangling and editing
of RNA molecules > 1000 nucleotides long.
产品编号 BC00396
名称 PERCH
类别 Crystallography
简介 PERCH (PEak reseaRCH) is an integrated software package offering
some powerful tools for research on 1D-NMR spectra.
PERCH takes advantage of 32-bit code, is running
on IBM/compatible PC (386 or higher, math. coprocessor) and
can
be accessed from a graphical user interface under WINDOWS
(picture) or command driven directly under DOS.
产品编号 BC00402
名称 DBCOMP
类别 Databases tools
简介 DBCOMP (and its counterpart DBUNCOMP) is based on the idea
of substitutional compression. Whereas
conventional substitutional compressors reduce
redundant phrases of rather small word-size, they do
not eliminate identical lines of consecutive entries,
which is a typical source of redundancy in
automatically acquired biological sequence data. In
contrast, DBCOMP is a line-oriented substitutional
compressor. By using a flexible word-size of one line,
the program replaces identical lines with a pointer to
the previous occurrence of those lines. The
compression scheme of DBCOMP is particularly suited to
compress databases that are highly redundant in the
annotation section as is typical of databases derived
from genome projects.
产品编号 BC00403
名称 KINEMAGE
类别 Molecular modelling and graphics
简介 Kinemages are "kinetic protein images" that accompany
many of the articles published in Protein Science. The
files with extension *.kin are ascii files that are
read by the program MAGE to produce kinemages. Kinemages
are produced from Brookhaven PDB formatted files using
the program PREKIN.
产品编号 BC00408
名称 SIM2
类别 Alignment Search software
简介 This program build local alignments of two sequences, each
of which may be hundreds of kilobases long.
SIM2 first constructs n best non-intersecting chains of
'fragments', such as all occurrences of identical 5-tuples
in each of two DNA sequences, for any specified n>= 1.
Each chain is then refined by delivering an optimal
alignment in a region delimited by the chain.
产品编号 BC00412
名称 WPDB
类别 Searching databases
简介 WPDB (the Protein Data Bank through
Microsoft Windows) is a PC based software package
comprising a compressed version of all or parts of the
PDB and a set of tools to query features of a single
structure or perform a comparative analysis on
multiple structures with emphasis on sequence
alignment and structure superposition.
产品编号 BC00418
名称 GELMANAGER
类别 Electrophoretic Gel analysis
简介 Gel Manager is a user friendly program which runs
in Microsoft Windows environment. It includes advanced
techniques of image processing along with sophisticated options
for data analysis. It can deal with different kinds of data
such
as: RFLP, RAMM, RAPD, microsatellites and other fingerprinting
techniques. Their capacities of data processing make of Gel
Manager a multipurpose program extremely useful for many types
of studies including the definition of genetic relationships,
taxonomy and classification , epidemiology, etc.
产品编号 BC00419
名称 PROTEIN DESIGNER
类别 Structure prediction
简介 Functions:
- Homology by P. Argos (3). [ALIMATF, HPLOTTAK, ALIGNTAK]
- Profiles according method described by Van Regenmortel (1).
- Secondary structure prediction and surface probability performed
based on method and statistical data proposed by P.Argos (2).
1. Van Regenmortel,M.H.V.(1989)Immunol.Today 10,266.
2. Argos,P.(1987). J.Mol.Biol. 193,331-348.
3. Argos,P.(1987). J.Mol.Biol. 193,385-396.
- Prosite search and molecular graphics.
产品编号 BC00420
名称 PRIMER-MASTER
类别 Oligomer design and synthesis
简介 Automatical search and selection of optimal primers and primers
pairs for various variants of PCR; Analysis of oligs supposed
to be used as PCR primers or hybridization probes; Editor for
comfortable typing-in new nucleotide sequences;
产品编号 BC00423
名称 Pol3scan
类别 WWW server
简介 Recognition of the eukaryotic internal control regions
A box and B box that are typical of tRNA genes and
tDNA-derived elements. The algorithm is based on the
statistical analysis of a database of 231 tRNA
promoter regions and makes use of weight matrices and
weight vectors for scoring. The program discriminates
between tRNA genes and related class III elements
(e.g. tDNA-derived SINEs) on the basis of the presence
of a transcriptional terminator signal and of the
base-pairing within the aminoacyl stem. The accuracy
of the prediction was estimated by scanning the
eukaryotic nuclear sequences present in the rel. 33 of
the EMBL database (65180 entries). The program
correctly identified 932 of 940 known tRNA genes
(0.85% of false negatives) with a false positive rate
of 0.0018%.
产品编号 BC00425
名称 WIMOVAC (Windows Intuitive Model of Vegetation Adaptation
to Climate Change)
类别 Plant photosynthesis
简介 Simulation of C3 and C4 photosynthetic response to climate
change
WIMOVAC is a modular modelling system designed to operate
on IBM PC's running Microsoft Windows. It is
designed to facilitate the modelling of various aspects of
plant photosynthesis with particular emphasis on the
effects of climate change. The package allows the
sophisticated control of simulation procresses through a
standardised Windows interface and provides automatically
formatted results as either tabulated data or as a range of
customisable graphs. WIMOVAC has been designed to be
highly interactive in nature and is suitable for research,
management and educational purposes.
产品编号 BC00426
名称 SAMSON
类别 Sequence analysis
类别 RNA analysis
类别 Protein structure analysis
简介 The SAMSON package is a tool for advanced analysis of
primary DNA, RNA and protein structures. The package consists
of 16 programs performing statistical analysis and comparison
of biopolymer sequences, search for homologies, translation
of
DNA and RNA sequences into amino acid sequences, splicing of
RNA sequences and restriction map construction, recognition
of
functionally related sites in biopolymer molecules, textual
analysis of DNA and RNA regulatory sites and prediction of
intermolecular hybridization sites in DNA and RNA molecules.
The SAMSON package consists of:
- 16 applied programs in form of executable modules under
MS-DOS v. 3.0 or higher;
- the Microsoft FORTRAN 5.0 source library containing
standard input-output and simple sequence processing routines;
- ASCII-files with manuals (in russian);
- helpfiles and other things that are need for learning
the software usage.
产品编号 BC00429
名称 Primer Design
类别 Oligomer design and synthesis
简介 PrimerDesign is a DOS-program to choose primer for PCR or
oligonucleotide probes. It is tailored to check known
sequences for repeats and unique sequences and subsequencly
to create prober primers according to this data. A lot of
constrains are available to meet your conditions. It can
handle up to 31500 base pairs.
Additional features: Unique sequences, repeats, restriction
sites
产品编号 BC00438
名称 PROMOTER SCAN
类别 Sequence analysis
简介 PROMOTER SCAN is designed to find putative eukaryotic Pol
II promoter
sequences in primary DNA sequence data. This program is experimental
in nature, and should be used as an experimental tool. PROMOTER
SCAN
is best used to locate regions in primary DNA sequence that
might be
good candidate regions to further test for promoter functionality.
At
this time, based upon test promoter and non-promoter sequence
sets,
the program recognizes approximately 70% of all EPD primate
promoter
sequences, with a false positive rate of about one in every
17,200
bases.
产品编号 BC00439
名称 RHMAP
类别 Genetic and Physical Mapping
简介 RHMAP is a program package for the
statistical analysis of radiation hybrid mapping data
产品编号 BC00440
名称 SIMLINK
类别 Genetic Linkage software
简介 SIMLINK is a program for evaluating the statistical power
of a proposed linkage study.
产品编号 BC00443
名称 ALP (Automated Linkage Pre-processor)
类别 Sequence_tools
简介 ALP is a Microsoft Windows application designed to analyse
microsatellite DNA fragments separated on an Automated Laser
Fluorescence sequencer (A.L.F., Pharmacia Biotech). ALP
will:
size the DNA fragments
remove PCR stutter and other artefacts
if provided with pedigree data, perform genotyping checks to
ensure a Mendelian inheritance pattern is followed
format the data for Lathrop's Linkage Program Package
产品编号 BC00444
名称 DERANGE2
类别 Phylogeny
简介 The program sorts permutations issued from two gene
sequences by using weigthed inversions, transpositions
and inverted transpositions.
产品编号 BC00446
名称 CROSSFIND
类别 Genetic and Physical Mapping
类别 Genetic tools
简介 Package to analyse CRI-Map chrompic output and detect well-
supported breakpoints in CEPH family data. Can produce multi-
page PostScript diagrams of the breakpoints.
产品编号 BC00453
名称 EMBL-Search
类别 Searching databases
简介 EMBL-Search is a free database query and retrieval program
for
the MS Windows 3.x or greater for use with the EMBL Sequence
Databases CD-ROM. Allows text queries of the PROSITE protein
pattern database, in addition to the EMBL nucleotide,
SWISS-PROT, LIGM.
产品编号 BC00455
名称 Statistical Routines
类别 Sequence display
简介 Routines written for the statistical package Splus in the
aim of a visual analysis of DNA sequences. Two types of
charts are produced, random walk plots and gap plots. For
details, see CABIOS, 11, pp. 503
产品编号 BC00456
名称 ICM (Internal Coordinate Mechanics)
类别 Molecular modelling and graphics
简介 ICM is a program for biomolecular structure
prediction, peptide folding, homology modeling, molecular
association (docking), molecular graphics and structure
analysis.
Applications: modeling by homology, peptide structure
predictions, protein-protein docking, ligand docking, domain
movements.
Shell: 15 objects types including vectors, matrices, molecular
selections, maps and shell-structures; full arithmetics with
the
objects; loops, conditions, functions, macros.
Energy: ECEPP/2, surface energy, entropy, grid energy.
Electrostatics: MIMEL, fast boundary element Poisson
electrostatics
Global optimization: Probability Biased Monte Carlo
minimization, loop sampling, pseudo Brownian Monte Carlo for
docking.
Sequence analysis: multiple sequence alignment, secondary
structure prediction
Graphics: wire, CPK, ball&stick, ribbon, accessible surface,
analytical molecular surface, general solid 3D objects, density
maps, countours, molecular movies.
Graphics output: Wavefront (.obj), vectorized postscript for
molecular images, compressed tiff.
Structure analysis: surface and volume calculations, secondary
structure assignment, structure superposition
Searches: fragment searches, spatial similarity searches
Mathematics: statistics, principal component analysis, 2D and
3D plots
产品编号 BC00457
名称 MatInd and MatInspector
类别 Sequence analysis
类别 Database and analysis
简介 MatInd is a simple but powerful method to derive a
matrix description of a consensus from a number of short sequences
on which the definition of an IUPAC code would be based.
MatInspector is a program that uses a large library of predefined
matrix descriptions of transcription factor binding sites
to locate matches in nucleotide sequences of unlimited length.
It assigns a quality rating to matches and thus allows a quality-
based filtering and selection of matches.
产品编号 BC00463
名称 SeqPup
类别 Sequence analysis
简介 SeqPup is a biological sequence editor and analysis program
usable on the common computer systems including Macintosh,
MS-Windows and X-Windows. It includes links to network
services and external analysis programs.
Features include
multiple sequence alignment editor
single sequence editor
read and write several sequence file formats
easy hand alignment features including colored bases and sliding
automatic multiple sequence alignment with ClustalW app
automatic gel fragment alignment to contigs with CAP app
phylogenetic analysis of alignments with fastDNAml and LSADT
apps
phylogenetic tree drawing with DrawTree and DrawGram Phylip
apps
consensus, reverse, complement, degap, and distance/similarity
operations
restriction maps
pretty print of alignments and sequences with boxed and shaded
regions.
translate dna to/from protein using various codon tables
find strings and ORFs
automatic preference saving
internet send mail and sequence analysis services by email
user-definable links to external analysis programs
产品编号 BC00464
名称 DOLINK
类别 Genetic tools
简介 DOLINK is a program we developed to help manage our genetic
data, particularly for linkage analyses. The user can use any
database with which they are familiar, and then export the data
to DOLINK which can then process it into a variety of different
for formats for LINKAGE, ESPA, CRIMAP or KIN. Examples are also
given of how the data can be exported directly from a database
to
programs such as SIMLINK, POINTER and PEDRAW.
Special features of DOLINK include: ability to target DOS or
Unix; runs either interactively or in batch mode; alleles can
be
checked for compatibility; alleles can be coded using numeric
and/or factor union notation; genotypes can be recoded to use
fewer alleles with minimal loss of information; affection loci,
quantitative loci, sex-linkage, liability classes and pedigree
loops are all handled correctly.
Other utilities are also provided to post-process LINKAGE output
to produce graphs of lod scores, and to provide input to HOMOG,
BTEST and FASTMAP.
产品编号 BC00467
名称 ABaCUS
类别 Statistical significance
类别 exon-protein correspondence analysis
简介 If you are interested in the possible
involvment of introns in protein gene evolution, this may
be of interest. ABaCUS is a no-frills program designed to
investigate the significance of some types of possible
correspondence between exons and units of protein
structure. This type of analysis takes the form of an
attempt to eliminate the reference ("null") hypothesis
that
the correspondence seen in the observed data is no greater
than expected by chance. The program continues to be
updated to allow more complex correspondence metrics and
reference gene models. There are also routines to simulate
the effects of deletion and so-called "sliding" of
introns.
产品编号 BC00470
名称 Primer Premier 4
类别 Oligomer design and synthesis
类别 Sequence format conversion tools
简介 Primer Design Software
Primer Premier 4 is now available for Power Macintosh and
Window 3.1, NT as well as Windows 95. Primers can be
designed for PCR, sequencing or hybridization probes
automatically or with full manual control.
From the selected pool of primers mutually compatible
Nested/Multiplex primers or pairs can be chosen.
Any primer can be mutated using the editing facility.
Full degeneracy is supported. Comprehensive analyis of
secondary structures as well as a table of properties
including melting temperature calculated using nearest
neighbor theory and optimal annealing temperature is
displayed for each primer.
The selected primers can be managed with the database
storage facility. The program even makes the primer
synthesis process painless by automatically creating an
order form addressed to the vendor of your choice.
Restriction enzyme analysis is available with multiple
output formats: table, annotated sequence or map. Functions
to edit the sequence and to translate it using standard or
any mitochondrial/organelle codon table is provided. Graphs
of melting temperature, internal stability and free energy
are available on-line as well as in printed format.
产品编号 BC00471
名称 C library tools
类别 Sequence analysis
类别 Sequence tools
简介 We offer C libraries for those who develop DNA analysis
tools for PC under MS DOS. Mini-database (so called data
handler) is designed in object-oriented manner. It can hold
different molecular-biological data in mode very
appropriate for C/C++ programmer. There is also common
virualization tool for the data stored in the data handler
format files.
产品编号 BC00474
名称 LALNVIEW
类别 Sequence analysis
类别 Protein sequence analysis
类别 Alignment editing and display
简介 LALNVIEW is a graphical program for visualizing local
alignments between two sequences (protein or nucleic acids).
Sequences are represented by coloured rectangles to give
an overall picture of their similarities. LALNVIEW is also
able to display sequence features (active site, domain,
motif, propeptide, etc.) along with the alignment. When
using LALNVIEW through our Web servers, sequence features
are automatically extracted from database annotations
(SWISS-PROT, GenBank, EMBL or HOVERGEN) and displayed with
the alignment. LALNVIEW is a useful tool for analysing
pairwise sequence alignments and for making the link
between sequence homology and what is known about the
structure or function of these sequences.
产品编号 BC00477
名称 Evolving
类别 Evolution
简介 Evolving is a program which demonstrates the effects of natural
selection.
In a game like atmosphere students assume the roles of grazing
elk,
pollinating hummingbirds, squirrel hunters or bird feeding on
peppered
moths. In doing so, they become the selective force which brings
about
genetic change in the populations with whom they interact
产品编号 BC00479
名称 TreeView
类别 Phylogeny
简介 View and print phylogenetic trees on Apple Macintosh
and Windows personal computers. Program reads NEXUS,
PHYLIP, ClustalW and Hennig86 tree files. Supports native
fonts and graphics formats (PICT and Windows metafiles),
print preview and drag and drop opening of files.
产品编号 BC00480
名称 ProMSED (Protein Multiple Sequence Editor)
类别 Protein sequence analysis
类别 Alignment Search software
类别 Alignment editing and display
简介 ProMSED, Windows 3.x/95 application for multiple protein
sequences alignment, alignment analysis and editing.
Reads several sequence formats, has main functions similar
to MS Word text editor. Automatic alignment is based on
ClustulV algorithm; manual alignment and visual analysis
are facilitated by group and block operations and amino
acid color coding reflecting their similarity in physico-
chemical, mutational and other properties.
产品编号 BC00484
名称 SorFind
类别 Sequence analysis
简介 Identification of protein coding regions in genomic DNA Sequence
SorFind is a DOS-based computer program that accepts a
DNA sequence as input in one of several formats, and produces
as output the same sequence in GenBank or EMBL format with
a feature table added to annotate the location of putative coding
exons. The program was first published in 1992 as a method to
search for first exons only, but has since been revised and
improved.
产品编号 BC00485
名称 PromFind
类别 Sequence analysis
简介 PromFind is a DOS-based computer program that accepts a
DNA sequence as input in one of several formats, and produces
as output the same sequence in GenBank or EMBL format with
a feature table added to annotate the location of putative
promoter regions. The program does not advise whether or not
a promoter is present, but rather assumes one is present and
makes one prediction as to its location per sequence segment
(specified by the user).
产品编号 BC00486
名称 RepFind
类别 Sequence analysis
简介 Identification of promoter regions in vertebrate DNA sequence
RepFind is a DOS-based computer program that accepts a
DNA sequence as input in one of several formats, and produces
as output the same sequence in GenBank format with a feature
table added to annotate the location and identity of common
repeat elements. As a default the program identifies known
human repeat elements, but it can be user-extended to identify
any sequence of interest to the researcher. Several options
allow control of the output, including a feature that replaces
all
repeat nucleotides with the letter "n" to facilitate
database
searches. The program may also be modified to identify and
exclude vector sequence.
产品编号 BC00487
名称 WinMGM
类别 Protein structure analysis
类别 Molecular modelling and graphics
简介 Visualisation and manipulation tools for biomolecules
(proteins and nucleic acids) and organic molecules.
Specific tools for proteins, allowing real-time manipulation
of molecules represented as CPK, stick and ball, ribbons
and cylinders. Specific colorations by atomic type,
atoms of a selected area, of an active site,...
Manipulation of a few molecules simultaneously.
Nearly exhaustive parametrisation of all visualisation
functions.
Raytracing function for quality drawings.
Specific build of peptides with geometry optimisation.
Measure and representation of hydrophobic and
electrostatic potentials.
Computation and representation of solvant accessible
surface.
False colors representation of atoms by energy level.
Computation and drawing of hydrogen bonds.
Ramachandran map, interdistances map,...
产品编号 BC00488
名称 GeneDoc
类别 Alignment editing and display
类别 Protein sequence analysis
类别 Phylogeny
简介 GeneDoc is a full featured Multiple Sequence Alignment Editor
and Shading Utility. GeneDoc is also intended to help you bring
your genetics research work to publication with lots of shading,
page and font layout features. This is a utility that reads
either
.MSF Multiple Sequence alignment files or can Import Fasta Format
files to be saved as a .MSF file project.
GeneDoc is an alignment editor, that is it allows you to Edit
the
Alignment so that different residues from each sequence are
lined
up with each other. This is accomplished by moving the residues
in
one (or all but one) sequence relative to the other sequences
by
inserting or deleting gaps. GeneDoc also features the exclusive
Grab and Drag mode, arranging residues like beads on a string.
A
residue editing mode is available to allow you to change the
residues values themselves. Built in DayHoff and BlockSum scoring
functions allow you to be sure your alignment changes are
improving the score. Scores can be determined either by a Sum
of
Pairs method or with the Phylogenetic tree support. GUI
implimentation makes it all so easy to use!
GeneDoc also provides a comprehensive range of Display Shading
Modes, functions and capabilities. Outlined below, these functions
give flexible ways to look at the data and to show important
concepts. Shading can even be done manually!
GeneDoc provides output many different ways. You can print
directly to the printer, export BitMaps, Text or MAC style Pict
files.
产品编号 BC00489
名称 DISTREE
类别 Phylogeny
简介 DISTREE computes pairwise distances (substitution rates)
of
aligned nucleotide sequences utilizing various models of base
substitution. Moreover it provides the user with information
on the goodness of fit of the models to the given set of
sequence data. Each of the models is implemented in two
variants, assuming identical and gamma distributed
substitution rates across sequence sites.
产品编号 BC00490
名称 ConsInspector
类别 Sequence analysis
简介 ConsInspector uses a precompiled library of extended weight
matrix descriptions (consensus profiles) of transcription
factor binding sites to scan nucleic acid sequences for
matches to these sites.
产品编号 BC00493
名称 MATRIX
类别 Image analysis
简介 QuantaVision Canada is happy to announce the
commercial release of MATRIX: a Gel Imaging software
package designed to locate and quantitate DNA/RNA/protein
bands from images derived from a variety of sources,
including: protein gels, PCR/DNA gels, RFLP gels,
Northerns, Southerns, and Westerns blots. Over a year in
development and use, the program was designed to provide
research scientists with a powerful and easy to use
Windows-based tool that exceeds the features of present-day
DOS and Windows-based programs.
Unlike most image analysis software, MATRIX
was designed to accept images from most CCD-based image
capturing systems and scanners, making it compatible with
virtually all existing systems. In addition, MATRIXs
comprehensive help file and tutorials make learning so easy
and intuitive, most users master the softwares capabilities
within a single hour.
产品编号 BC00495
名称 BlueGene
类别 Searching databases
简介 BlueGene uses a fast neural network for sequence similarity
searches in Genbank and SWISS-PROT databases.
BlueGene also includes graphically tools for sequence
editing and analysing.
BlueGene uses given and new sequence features to annotate
the sequence editor and the map.
产品编号 BC00497
名称 Sequin
类别 Sequence format conversion tools
简介 Sequin is a stand-alone software tool developed by the NCBI
for submitting entries to the GenBank, EMBL, or DDBJ
sequence databases. It is capable of handling simple
submissions which contain a single short mRNA sequence, and
complex submissions containing long sequences, multiple
annotations, segmented sets of DNA, or phylogenetic and
population studies.
产品编号 BC00500
名称 DnaSP
类别 Population Genetics
简介 DnaSP is a software package for Windows that
performs extensive population genetics analysis on DNA
sequence data.
DnaSP estimates several measures of DNA sequence
polymorphism within and between populations, and linkage
disequilibrium, recombination, gene flow, and gene conversion
parameters.
DnaSP can also conduct some neutrality tests: Fu and
Li's; Hudson, Kreitman and Aguade; McDonald and Kreitman;
and Tajima's tests.
DnaSP allows performing several analyses by the sliding window
method, and also to obtain graphic representations.
Input: Aligned DNA sequences in NBRF/PIR, MEGA, and NEXUS
file formats.
Output: the results are displayed in tables and graphs. The
output can be either sent to the printer or saved in a file.
The program can handle a large number of sequences (hundreds)
of thousands of nucleotides each.
产品编号 BC00507
名称 NJPLOT
类别 Protein sequence analysis
类别 Sequence analysis
类别 Phylogeny
简介 NJPLOT is a phylogenetic tree drawing program that handles
files describing trees by the nested parentheses method
(e.g. PHYLIP-built trees).
Features:
A graphical interface allows to re-root a tree anywhere and
to swap branches.
Bootstrap values are displayed next to internal branches.
Branch lengths can be optionally displayed.
Tree plots can be saved to a PostScript file (a PICT file
on Macintosh) for printing.
产品编号 BC00512
名称 GEPASI
类别 Population Genetics
类别 Metabolic regulation
简介 Gepasi is intended for the simulation of the
kinetics of systems of chemical and biochemical reactions.
Gepasi is able to simulate the steady-state and time
course behaviour of reactions in several compartments of
different volumes. The user supplies the program with
information about the stoichiometric structure of the
pathway, kinetics of each reaction, volumes of the
compartments and initial concentration of the chemical
species. The program then builds the implicit differential
equations and solves them, both for steady state and time
course. Results can be plotted in 2D and 3D graphs directly
from the program (by using gnuplot, included here). Steady
states are analysed with metabolic control analysis (MCA)
and linear stability analysis (eigenvalues of the
Jacobian). Data is output in ASCII columnar files that can
easily be loaded in other programs.
产品编号 BC00519
名称 ONIX
类别 Protein structure analysis
类别 Molecular modelling and graphics
类别 Image analysis
简介 PC-based program for Windows, ONIX, allows
users to examine proteins with known 3D structure from PDB.
This program was designed for structure investigation of
ligand binding site in proteins. The last one is a
combination of certain fragments of protein sequence. Its
examination requires active participation both of human and
computer in the process of investigation. ONIX is an
interactive software with high-performance interface, fast
3D molecular graphics and analysis of water-accessible
surface. This program was designed based on protein
structure hierarchy. Analysis of molecular surface makes
possibly to find all elements of ligand binding site.
产品编号 BC00522
名称 Primers! for the WWW
类别 Sequence analysis
类别 Genetic tools
类别 Oligomer design and synthesis
类别 WWW server
SERVER http://www.williamstone.com/primers
Free oligonucleotide design and analysis online.
产品编号 BC00525
名称 TFPGA (Tools for population genetic analyses)
类别 Population Genetics
简介 TFPGA is a windows program for the analysis
of allozyme and molecular population genetic data. The
program calculates simple descriptive statistics, genetic
distances, and F-statistics. It also performs tests for
Hardy-Weinberg equilibrium, population differentiation and
performs UPGMA clustering and Mantel Tests.
产品编号 BC00528
名称 Bielefeld University Bioinformatics Server
类别 WWW server
简介 BibiServ is both, a fast computer to run web-based
bioinformatics software and an integration point for
the bioinformatics activities at Bielefeld University.
作者 multiple authors
产品编号 BC00530
名称 Band Leader
类别 Sequence tools
类别 Protein sequence analysis
类别 Genetic tools
Band Leader is software for the PC Windows operating environment.
简介 It is very easy to use and requires only basic Windows skills.
With Band Leader you process your gel images to extract data
arranged in lanes or in spots.
You may create graphs representing data along lanes which you
may later
process to extract band information.
You may create Spot documents, representing single spots on
the Gel
image or use the Grid tool to extract a group of Spots.
Band Leader data can be exported as flat text file or as Spreadsheet
data.
Band Leader is an MDI application, thus you may load more than
one set of images to process at a time.
产品编号 BC00532
名称 CODONTREE
类别 Sequence analysis
简介 The classic triplet code responsible for the translation
of a mRNA sequence into the amino acid sequence of a
protein was the first deciphered code of the genetic
language. Owing to the degeneration of the genetic code,
different triplets (codon families) can code for the
same amino acid. As soon as the first nucleotide
sequences were produced, it was immediately clear
that for a given gene the usage of different synonymous
codons was not random but rather species specific,
and also linked to its expression and/or to the
genetic compartment where it was located.
The algorithm CODONTREE has been devised in order to
investigate the linguistic properties of coding regions,
that is, their codon strategy.
CODONTREE is able to determine:
codon usage table for a set of protein coding genes;
gene relationship on the basis of codon usage similarity;
compositional features of protein coding genes
(e.g. bases composition at various codon positions).
产品编号 BC00533
名称 DNAmend
类别 Sequence analysis
简介 DNAmend is cloning software. That means, it may serve
lab-workers in molecular biology and genetic engineering to
monitor the DNA-cloning process. The PC routine provides
on-line control on the steps of a cloning protocol -
including the selection of the vectors and fragments, their
processing by restrictase digestion, subsequent ligation,
and the analysis of the cloned DNA.
The software is designed to accept files containing DNA
sequence information in any file format based on PC-text.
A set of pull-down menu commands enables the user to change
the mode of viewing the DNA-sequences, print them out, and
above all manipulate them. One can search DNA sequences for
restriction sites, open reading frames and certain sequence
patterns, translate the sequences and simulate Restriction,
Ligation or End modification on-line.
One may export maps of the DNA-sequences via clipboard into
other windows applications to prepare them for publication.
The program contains a detailed on-line help.
产品编号 BC00535
名称 VECTOR NTI
类别 Sequence display
类别 Sequence editor
类别 Sequence analysis
类别 Genome Mapping Databases
类别 Restriction maps
简介 Software package for molecular biology.
Vector NTI is a software package to aid
molecular biologists, genetic engineers, students, and
others in the study, manipulation, and creation of
biological molecules. It's extremely helpful in supporting
your everyday lab work, making it mistake free and saving
enormous amounts of your time. Using vector NTI you can:
automatically create an optimum cloning strategy for
construction and design of new genetic molecules, perform
advanced PCR, oligo and primer analysis, organize your
biological data (molecules, oligos, ect.) using a
professional database, create excellent publication quality
graphical molecule maps, transfer changes made to molecules
in child/parent trees, run dynamic electrophoresis, predict
runtime, connect to Oracle backend database and much much
more. Free demo at informaxinc.com
产品编号 BC00536
名称 Anemona
类别 Enzyme kinetics
简介 ANEMONA.XLT is an EXCEL template for
calculation of enzyme kinetic parameters by non-linear
regression techniques. The tool is accurate as well as easy
to use and modify.
The different worksheets each deal with a
different mathematical model. These sheets can be filled,
used and saved in the same file or they can be copied and
pasted into other EXCEL files, where they will retain the
same properties as in the original.
The models implemented are those
corresponding to mono- or pseudo-monosubstrate reactions
and the most common bisubstrate reactions:
Michaelis-Menten, Double Michaelis-Menten, Hill model,
Substrate Inhibition, the linear cases of reversible
inhibition
(Competitive, Incompetitive, Non-Competitive
and Mixed Competitive-Incompetitive inhibition) and
Ping-Pong, Ordered and Random bisubstrate mechanisms. Also,
a weighted linear model has been implemented.
If convergence is reached, the estimated
values of the kinetic parameters are displayed, together
with their standard error, covariances, final value of the
Y function, the variance of fit and a X2-test of the fit.
At the same time, graphs showing the
original data and the fitted function versus
the independent variable (concentration of substrate or
inhibitor) and the residuals versus the independent
variable are also provided. To aid in analysis of
residuals, confidence limits for the residuals are also
plotted.
产品编号 BC00537
名称 DynaFit
类别 Metabolic regulation
类别 Enzyme kinetics; Equilibrium binding
SERVER http://www.biokin.com/dynafit/index.shtml
简介 The main purpose of the program DynaFit is to perform
nonlinear least-squares regression of chemical kinetic,
enzyme kinetic, or ligand-receptor binding data.
The experimental data can be either initial reaction
velocities in dependence on the concentration of
varied species (e.g., inhibitor concentration vs. velocity),
or the reaction progress curves (e.g., time vs.
absorbance), or the composition at equilibrium in dependence
on the total concentrations (e.g., protein-DNA complex
concentration vs. total protein).
产品编号 BC00540
名称 Migrate
类别 Population Genetics
简介 Migrate is a maximum likelihood estimator
for migration rates and effective population sizes using an
extension of coalescence theory. The current version uses a
simple two population model with 4 parameters: population
sizes for each subpopulation and migration rates for each
subpopulation. Data from several loci can be combined
either by assuming the mutation rate is constant between
loci, or that the mutation rate is following a Gamma
distribution. Input data can be either sequence data,
microsatellite data, or enzyme electrophoretic data.
产品编号 BC00541
名称 Plasmid Premier
类别 Restriction maps
简介 PLASMID PREMIER is a fully featured vector analysis and
publication quality graphics tool. It provides vector
analysis tools including restriction enzymes, motifs,
open reading frames, and features. It allows complete
restriction enzyme analysis including user defined enzymes,
enzyme filtering by overhang and cutting frequency, and a
databases of over 300 enzymes. Motif analysis automatically
locates motifs such as TACCC-binding and T-antigen sequences
and supports user defined motifs. ORF analysis locates all
open reading frames in both the sense and anti-sense
direction. Start and stop codons are editable allowing
support of mitochondrial codon tables. Features from GenBank
files are automatically read and shown on the plasmid.
In addition to automatic analysis, enzymes, motifs, and
features can be added manually. The user can set position,
font, and color. Default styles can be set and modified.
Styles can be copied and pasted between objects. Plasmids
can be output in Windows bitmap or Mac PICT formats, or cut
and pasted through the clipboard.
产品编号 BC00542
名称 Spectrum
类别 Sequence analysis
类别 Phylogeny
简介 SPECTRUM is a new Macintosh. and Microsoft. Windows. program
designed to read in phylogenetic 4-state or binary data in
NEXUS format, and display the bipartition spectra
corresponding to the data.
It can also be used to find the tree whose expected spectrum
is closest to the observed spectrum (the "closest tree").
SPECTRUM outputs spectra in Microsoft. Excel? format as
tab-delimited text files and trees as TREEVIEW files.
产品编号 BC00543
名称 Visual BLAST (and Visual FASTA)
类别 Protein sequence analysis
类别 Alignment editing and display
简介 To facilitate and accelerate BLAST and FASTA output results,
we present, for the first time, two easy-to-use programs
designed for interactive analysis of full BLAST and FASTA
output files containing protein sequence alignments. These
programs, Visual BLAST and Visual FASTA, run under Microsoft
Windows 95 or NT computers. They are based on the same
intuitive graphical user interface (GUI) with extensive
viewing, searching, editing, printing and multithreading
capabilities. These programs improve the browsing of
BLAST/FASTA results by offering a more convenient
presentation of these results. They also implement on a
computer several analytical tools which automate a manual
methodology used for detailed analysis of BLAST and FASTA
outputs. These tools include a pairwise sequence alignment
viewer, a Hydrophobic Cluster Analysis plot alignment
viewer and a tool displaying a graphical map of all
database sequences aligned with the query sequence.
In addition, Visual BLAST includes tools for multiple
sequence alignment analysis (with an amino acid patterns
search engine), and Visual FASTA provides a GUI to the
FASTA program.
产品编号 BC00468
名称 Cyrillic 2
类别 Pedigree Analysis Package
简介 For pedigree drawing and managing genetic data.
Cyrillic brings together all the tools for drawing family
pedigrees and managing genetic data. Cyrillic will store
information about genetic disease markers and patient
details and assign haplotypes to DNA genotypes.
Pedigrees and marker data can be imported from many sources,
and data can be sent to risk calculation programs.
Working with individuals and adding first degree relatives,
Cyrillic pedigrees are drawn on a Windows PC much as they
would on paper but with all the data stored. Cyrillic抯
high-quality output is perfect for papers, reports and
presenting pedigrees to patients.
Commercially available at *399.
产品编号 BC00476
名称 SEQIO
类别 Sequence format conversion tools
简介 SEQIO is a C/C++ package for reading and writing sequences
in
a number of different formats, including GenBank, EMBL, PIR,
FASTA, IG/Stanford, Clustal, PHYLIP and others. It is available
for Unix and Windows NT/95 systems.
Including in the distribution is a file format conversion program,
fmtseq, which is a reimplementation and extension of Don Gilbert's
readseq program, and a fixed-width motif searching program.
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