Molecular Biology Software

Available to the NIH Research Community




Genomic Software Supported by CBEL, BIMAS and made available through ALW workstations running AFS.

Categories

  1. Comprehensive Genomic Sequence Analysis Packages/Suites
  2. Genetic Mapping Tools/Utilities
  3. Linkage Analysis Tools
  4. Primer Selection Tools
  5. Sequence Similarity, DB Search Tools
  6. Sequence Database Access Tools
  7. Sequence Analysis Tools
  8. Misc. Utility Tools

  1. Comprehensive Genomic Sequence Analysis Packages/Suites
    GCG Version 8.1 dated August 1995:
    Commercial software package, based on the Wisconsin Package, developed by Genetics Computer Group, Inc. Databases available to be used with GCG are:
                       GenBank            Release 95.0 ( 6/96)
                       EMBL (Abridged)    Release 46.0 ( 3/96)
                       PIR-Protein        Release 48.0 ( 3/96)
                       SWISS-PROT         Release 33.0 ( 3/96)
                       PROSITE            Release 13.0 (12/95)
                       Restriction Enzymes (REBASE)    ( 6/96)
        
    GCG Version 8.0 (UNIX) documentation is available on-line for GCG-licensed institutions. NIH users can browse this documentation and non-NIH users are directed to GCG WWW Pages from Yeshiva University.

    Availability: Solaris 2.4 platforms.
    SPECIAL NOTE: Please be advised that SunOS 4.1.3 platforms are running GCG 7.3 and hence are using very old version of databanks.

    GDE Version 2.2a dated November 28, 1993:
    The Genetic Data Environment is part of a growing set of programs for manipulating and analyzing "genetic" data. It differs in design from other analysis programs in that it is intended to be an expandable and customizable system, while still being easy to use. GDE provides an X Windows based GUI to a large number of publicly available programs for sequence analysis. The software used SUN's XVIEW, efforts are underway to port the software to MOTIF.

    Sequence analysis functions included with this package:

    • ClustalV (cluster multiple sequence alignment)
    • MFOLD (RNA secondary prediction)
    • Blast (Basic Local Alignment Search Tool)
    • FastA (Similarity Search)
    • Assemble Contigs (CAP Contig Assembly Program)
    • Lsadt (Least squares additive tree analysis)
    • Count (distance matrix calculator)
    • Treetool (Tree drawing/manipulation)
    • Readseq (format conversion program)

    GDE itself was developed by Steve Smith, currently with Millipore Imaging Systems. Numerous others provided or contributed to the individual analysis programs included with GDE.

    GDE 2.2 manual is available both in text and postscript format. Also, Lachlan Bell of Daresbury Laboratory, Warrington in U.K. maintains a HTML document for GDE.

    The following paper (to appear in CABIOS), contains information describing GDE and it's development.

    S.Smith, R. Overbeek, C.R. Woese, W. Gilbert and P. Gillevet, The Genetic Data Environment: An Expandable GUI for Multiple Sequence Analysis.

    Availability: SunOS 4.1.3 platforms.

  2. Genetic Mapping Tools/Utilities
    CRI-MAP Version 2.4 dated March 17, 1994:
    The main purpose of CRI-MAP is to allow rapid, largely automated construction of multilocus linkage maps (and facilitate the attendant tasks of assessing support relative to alternative locus orders, generating LOD tables, and detecting data errors).

    Crimap is developed by Phil Green of Dept. of Genetics, Washington University School of Medicine.

    CRI-MAP 2.4 documentation is available in text, HTML and postscript formats.

    CRIMAP tutorial is also on-line as part of EMBnet Biocomputing Tutorials

    Availability: SunOS 4.1.3 platforms.

    QUICKMAP Version 2.0, Dated October, 1995:
    QUICKMAP is a compact database and navigation tool for the physical map of the human genome. The backbone of the map is the Genethon 1993 genetic map. This includes 2067 STS genetically mapped to a chromosomal assignation and a genetic position.

    This package includes:

        quickmap   - X windows based navigation tool
        infoclone  - a query program 
        show_map   - support program for using navigation tool in batch
        locus      - support program for using navigation tool in batch
        path       - support program for using navigation tool in batch
        clonespath - support program for using navigation tool in batch
    

    QUICKMAP was developed at GENETHON, France by P.Rigault and E. Poullier

    Availability: SunOS 4.1.3 and Solaris 2.4 platforms.

    SIGMA Version 2.2, Dated March 21, 1994:
    SIGMA (System for Integrated Genome Map Assembly) is a software tool for creating, maintaining and editing integrated genome maps. SIGMA is produced by the Human Genome Information Resources as Los Alamos National Laboratory and is freely available on request (although all rights are reserved).

    Documentation on SIGMA is available from National Center for Genome Research and also from Baylor College of Medicine (Help given by menu category of the program).

    Availability: SunOS 4.1.3 platforms.

  3. BIMAS Genetic Linkage Analysis Tools

  4. Primer Selection Tools
    OSP dated November 11, 1991:
    Oligo Selection Program (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) melting temperatures; 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.

    osp is a text-only version and ospX is having an interactive X windows graphic interface. These programs are developed by LaDeana Hillier and Phil Green at Washington University Medical School, St. Louis.

    Additional information of osp can be found in:
    Hillier, L. and Green, P. (1991). "OSP: A computer program for choosing PCR and DNA Sequencing Primers," PCR Methods and Applications, 1, 124-188.

    Availability: SunOS 4.1.3 platforms.

    Primer Version 0.5 dated April 27, 1992:
    PRIMER is a computer program for automatically selecting PCR primers. PRIMER tests oligos for annealing temperature, complementarity to genomic repeat sequences (e.g. Alu), ability to form primer-dimer, and other criteria. Importantly, PRIMER's annealing temperature calculation is based on thermodynamic parameters (with the base stacking term dominant), and is far more accurate than calculations based on GC/AT ratios.

    PRIMER was developed and produced by Steve Lincoln, Mark Daly, and Eric Lander of MIT center for Genome Research and Whitehead Institute for Biomedical Research.

    PRIMER manual can be read on-line. More information about Primer software can be obtained from MIT Genome Center.

    Availability: SunOS 4.1.3 platforms.

  5. Sequence Similarity, DB Search Tools
    Blast Output Browser dated August 22, 1994:
    Blast Output Browser, BoB, is an an X window application to browse through blast output results from either NCBI Blast server, DNA workbench server or the BLITZ email server in an environment where a lot of BLAST processing is done (for example in cDNA projects). One or two blast output results can be browsed simultaneously. While browsing through results, you can immediately view alignments, blast results file, and also the actual database entry.

    BoB program is developed by John Powell and Rao Parasa of CIT at NIH and is available in the public domain by anonymous ftp from ftp-bimas.dcrt.nih.gov.

    User's guide and man page are available for BoB.

    Availability: SunOS 4.1.3 platforms and helix.

    CLUSTAL W version 1.4 dated September 23, 1994:
    Clustal W is a general purpose multiple alignment program for DNA or proteins.

    Multiple alignments are carried out in 3 stages:

    1. All pairs of sequences are aligned separately (pairwise alignments) in order to calculate a distance matrix giving the divergence of each pair of sequences;
    2. A guide tree (like a phylogenetic tree) is constructed from the distance matrix;
    3. The sequences are progressively aligned according to the branch order in the guide tree.

    Clustalw program is a major update and rewrite of clustalv program, distributed with GDE (Genetic Data Environment) package. Clustalw is produced by Julie D. Thompson, Toby Gibson of European Molecular Biology Laboratory, Germany and Desmond Higgins of European Bioinformatics Institute, Cambridge, UK. Algorithmic improvements over clustalv:

    1. Individual weights are assigned to each sequence in a partial alignment in order to downweight near-duplicate sequences and upweight the most divergent ones.
    2. Amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned.
    3. Residue specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure.
    4. Positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions.

    CLUSTALW Reference: Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994), CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice, Nucleic Acids Research, submitted, June 1994.

    Availability: SunOS 4.1.3 platforms.

    Fasta Version 2.0u6, September 1996:
    This program package contains sequence database search programs:
    • Library search programs: FASTA, TFASTA, FASTX, TFASTX, SSEARCH
    • Local homology programs: LFASTA, PLFASTA, PCLFASTA, LALIGN, PLALIGN, FLALIGN
    • Statistical significance: PRDF, RELATE, PRSS
    • Global alignment: ALIGN, ALIGN0
    • Utility programs: BESTSCOR, FROMGB
    In addition, included are several programs for protein sequence analysis, including a Kyte-Doolittle hydropathicity plotting program (GREASE, TGREASE), and a secondary structure prediction package (GARNIER).

    Fasta program package is produced by William R. Pearson and has the copyright 1988, 1991, 1992, 1994, 1995, 1996 by William R. Pearson and the University of Virginia. All rights are reserved.

    FASTA package documentation is here and also an interpretation of FASTA output is provided by Fredj Tekaia, tekaia@pasteur.fr.

    Availability: SunOS 4.1.3 and Solaris 2.4 platforms.

    Local BLAST dated March 03, 1994:
    BLAST (Basic Local Alignment Search Tool) is the heuristic search algorithm employed by the programs blastp, blastn, blastx, tblastn, tblastx and blast3.

    NOTE: To differentiate the local BLAST programs from their network counterpart, an 'l' is prepended to the name of each local blast program.

    The programs are used for the following purposes:

    • lblastp - to compare an amino acid query sequence vs. a protein sequence database.
    • lblastn - to compare a nucleotide query sequence vs. a nucleotide sequence database.
    • lblastx - to compare a nucleotide query sequence translated in all reading frames vs. a protein sequence database.
    • ltblastn - to compare a protein query sequence vs. a nucleotide sequence database dynamically translated in all reading frames.
    • ltblastx - to compare a nucleotide query sequence translated in all reading frames vs. a nucleotide sequence database translated in all reading frames.
    • lblast3 - protein database search for three-way alignments, using the BLAST pairwise search algorithm.

    Databases to be searched by local blast programs must first be processed either by the program setdb for protein sequence databases (re: blastp and blastx) or the program pressdb for nucleotide sequence databases (re: blastn, tblastn and tblastx). The input database format is FASTA/Pearson.

    Point accepted mutation (PAM) matrices of various generations can be produced automatically with the pam program. The output can be saved in a file whose name is then specified in the M=filename option of a blastp, blastx, or tblastn query. Also various BLOSUM matrices are supplied.

    BLAST programs are developed at the NCBI, NIH. Complete information about BLAST is available from BLAST notebook

    BLAST Reference: Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman (1990). Basic local alignment search tool. J. Mol. Biol. 215:403-410.

    Availability: SunOS 4.1.3 platforms.
    NOTE: NO LOCAL DATABASES ARE PROVIDED. Network BLAST (or BLAST2) is the recommended BLAST for searches against the public databases.

    BLAST2 dated July 26, 1996:
    BLAST2 programs, successor of Network BlAST programs, are rapid sequence database search programs using the BLAST algorithm. The network blast provides a client set of programs which access the NCBI BLAST server, which in turn, performs the actual search of the databases. BLAST2 utilizes a general service discovery and request facility called Dispatcher (from network entrez concept). Network BLAST is the recommended BLAST for searches against the public databases.

    BLAST2 programs are developed at the National Center for Biotechnology Information (NCBI), a division of the National Library of Medicine (NLM).

    Output from BLAST server is explained by Fredj Tekaia, tekaia@pasteur.fr. Complete information about BLAST is available from BLAST notebook

    BLAST Reference: Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman (1990). Basic local alignment search tool. J. Mol. Biol. 215:403-410.

    Availability: SunOS 4.1.3 and Solaris 2.4 platforms.

    SIM dated May 05, 1992:
    SIM is a program for finding local similarities using dynamic programming techniques. This program finds non-intersecting alignments between two sequences or within one sequence. The alignments are reported in order of similarity score, with the highest scoring alignment first.

    SIM program is copyright (c) 1990,1991 by Xiaoqiu Huang (Michigan Technological University) and Webb Miller (The Pennsylvania State University).

    SIM reference: Xiaoqiu Huang and Webb Miller. A Time-Efficient, Linear-Space Local Similarity Algorithm. Advances in Applied Mathematics, 12: 337-357, 1991

    Availability: SunOS 4.1.3 platforms.

  6. Sequence Database Access Tools
    GDB Interface
    GDB/OMIM is front-end software for Human Genome Database hosted at the Johns Hopkins University School of Medicine, Baltimore. GDB (Genome Database) is a consensus database to support mapping effort through international collaboration and is updated continuously. Data is taken from:
    • Literature and other databases
    • Human Genome Mapping Workshops
    • Chromosome-specific Workshops
    • Genome Centers and National Laboratories
    • GDB Editors
    • Direct Author Submission
    GDB uses the SYBASE database management system licensed from Sybase, Inc., Emeryville, California and requires OpenClient Library License for the front-end.

    OMIM is the continuously updated online version of Dr. Victor A. McKusick's catalog MENDELIAN INHERITANCE IN MAN (MIM). Because this knowledge-base is updated daily, the entries may differ from the most recently published version of the book. MIM catalog contains Autosomal Dominant, Autosomal Recessive, X-Linked, Y-Linked, and Mitochondrial Phenotype modes of inheritance. OMIM comes with an IRx Information Retrieval System that is currently being developed by the Information Technology Branch of the Lister Hill National Center for Biomedical Communications at the National Library of Medicine.

    More information about GDB and OMIM can be read from GDB Homepage at Johns Hopkins University. Also, there is an on-line course about GDB and OMIM by David Featherston.

    Availability: SunOS 4.1.3 platforms.
    NOTE: For ALW workstation users, gdb by default will start GNU debugger application.

    Network Entrez 5.002 dated July 26, 1996:
    Entrez is a molecular sequence retrival system devloped at NCBI, a division of the National Library of Medicine (NLM). Entrez porvides 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, DDJB, PIR, SWISS-PROT, PRF and PDB.

    Network Entrez is a client program, which requires a network server to access the databases. The Network Entrez installed on ALW workstations uses the NCBI network servers for accessing the databases.

    More information about Entrez Browser is available from NCBI.

    Availability: SunOS 4.1.3, Solaris 2.4 and SGI 5.2 platforms.

  7. Sequence Analysis Tools
    Signal Scan Version 4.05 dated March 15, 1996:
    Signal scan is a program developed to facilitate the analysis of DNA sequences for known eukaryotic signals. It incorporates the data from Dr. David Ghosh's Transcriptional Factor Database. What SIGNAL SCAN does is to find homologies of published signal sequences in your sequence, most of these being transcriptional elements. It cannot, at this time, predict what it finds has any meaning. The interpretation of those results are up to you. Most signal elements found probably will not have any meaning, as the elements are in the wrong milieu, wrong cell type, or wrong organism. Consequently, there will be many more erroneous signals found by SIGNAL SCAN than significant ones.

    Sigscan program is developed and produced by Dan S. Prestridge of University of Minnesota at St. Paul (danp@molbio.umn.edu). Although it is free, it is Copyright (c) 1993, 1994, 1995, 1996 by Dan S. Prestridge.

    SIGSCAN reference: Prestridge, D.S. (1991) SIGNAL SCAN: A computer program that scans DNA sequences for eukaryotic transcriptional elements. CABIOS 7, 203-206.

    Availability: SunOS 4.1.3 platforms.
    NOTE: SIGSCAN program is started by typing signal. Users are advised to use web version of signal.

    xgrail Version 1.3b dated September 27, 1995:
    xgrail is a client-server implementation of a group of analysis tools for sequence exploration and gene discovery. This package allows the user to find protein coding regions in anonymous DNA sequences, to assemble gene models, translate part or all of these models, and search these translations against various databases. It also provides information about GC content, functional site identification (splice junctions, poly A sites, Pol II promoters, and CpG Islands) and the location of a variety of repetitive DNA sequences.

    xgrail is produced by M.B.Shah, X.Guan, J.R.Einstein, S.Matis, Y.Xu, R.J.Mural and E.C.Uberbacher of informatics group at Oak Ridge National Laboratories.

    More information on xgrail can be found at the official xgrail site. Here is a blurb on grail from Oak Ridge National Laboratories.

    Availability: SunOS 4.1.3 platforms.

  8. Miscellaneous Utility Tools
    btab Version 4.06 dated October 12, 1994:
    BTAB is a program to parse BLAST output into tab delimited fields. It was originally written by Mark Dubnick of NINDS at NIH.

    Documentation for BTAB can be read from here. Also, current version of BTAB is available by anonymous ftp from ftp-bimas.dcrt.nih.gov.

    Availability: SunOS 4.1.3 platforms.

    msblast dated July 13, 1994:
    msblast is an X-windows interface utility to do BLASTing on multiple sequences. This program uses network BLAST programs.

    msblast program was developed and produced by Rao Parasa and John Powell of CIT at NIH and is available in the public domain by anonymous ftp from ftp-bimas.dcrt.nih.gov.

    Man pages are available for msblast.

    Availability: SunOS 4.1.3 platforms (by request).

    ReadSeq dated April 15, 1996:
    Readseq program converts between various nucleic/protein sequence formats. Data files may have multiple sequences. Readseq is particularly useful as it automatically detects many sequence formats, and interconverts among them.

    Readseq program is developed and produced by Don G. Gilbert of Indiana University at Bloomington. Readseq is copyright (c) 1990 by Don G. Gilbert.

    Readseq help and man pages are available.

    Availability: SunOS 4.1.3, Solaris 2.4 and SGI 5.2 platforms.

    Sequence extractor dated June 24, 1994:
    exs is a small utility program that takes a file of sequences in FASTA format and parse it according to the number of sequences you want per parsed section. After parsing, the groups of parsed sequences can be sent to another executable (can be a shell script or a program).

    exs program was developed and produced by Joshua Yulish and John Powell, NIH. Read the man pages for more information.

    Availability: SunOS 4.1.3 platforms.

    Translate dated February 27, 1995:
    Translate program translates selected sequences from DNA/RNA to Amino Acid. This program can either be used with a packed FASTA format sequence or GDE format sequence. The frame number is appended to the sequence name as '.#'

    This translate program is a modified version of 'Translate' program, distributed with GDE (Genetic Data Environment) package. The present version is produced by John C. Kelley and Rao Parasa of CIT at NIH.

    This program is available in the public domain by anonymous ftp from ftp-bimas.dcrt.nih.gov (128.231.129.60).

    Availability: SunOS 4.1.3 platforms.


Go back toBIMAS homepage
BioInformatics and Molecular Analysis Section
CBEL, CIT, NIH

Feedback on BIMAS software or this document should be addressed to:
John I. Powell, jip@helix.nih.gov (OR)
V. Rao Parasa, parasa@nih.gov