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[EBI] (G.J. Barton) “ALSCRIPT takes a multiple sequence alignment in AMPS block-file format and a set of formatting commands and produces a PostScript file that may be printed on a PostScript laser printer, or viewed using a PostScript previewer.”
AMAS: Analyze Multiple Alignments of Protein Sequences
[EBI] Allows the identification of functional residues by comparison of sub-groups of sequences arranged on a tree.
[EBI] A suite of programs for multiple protein sequence alignment. The programs include options to incorporate non-sequence information such as secondary structures, and also implements flexible pattern matching and database scanning options.
Analytical Biostatistics Section
[NIH] The ABS offers downloadable software and servers in the areas of sequence analysis, protein structure prediction, ligand binding, and gene expression.
Aneda, formerly Edinburgh Biocomputing Systems, develops software tools for biologists including the MPSRCH(tm) suite of Smith-Waterman sequence analysis programs which run on general purpose hardware at BLAST-like speeds.
[Institute of Biology and Chemistry of Proteins] (ANalyse THE PROTeins) This free software application integrates into a single package most of the methods designed forprotein sequence analysis. Methods include: Sequence information,Sequence edition, dot matrix plot,FASTA/BLAST, sites/signatures detection, physico-chemical profiles, secondary structure prediction, helical wheel projections, multiple alignments,prediction of signal peptide and cleavage sites, 3D display of molecules, amphiphilicity, andtitration curve.
Artemis sequence viewer
[The Sanger Centre, U. K.] The Artemis sequence viewer and annotation tool allows visualization of DNA sequence features and sequence analysis, including six-frame translation. Artemis can read complete EMBL and GENBANK database entries or sequence in FASTA or raw format. Written in Java, Artemis is available for UNIX, Macintosh or MS Windows.
B Molecular Modeling
[Scripps Institute] Formerly called Biomer, this Java applet builds molecular models to order. Designate components like DNA bases and amino acids to assemble into one molecule. The program also offers functions for energy minimization and molecular dynamics.
Biocompare, The Consumer Guide for the Life Scientist, offers information such as technical specs, prices, and peer reviews of life science products and services (including Bioinformatics). Biocompare also offers informationabout the latest technologies in the life science community and provides scientists with a list of companies that offer discounts for setting up new laboratories.
Bioinformatics & Pattern Discovery
[IBM] Information and bioinformatics related servers developed at IBM. Services include sequence pattern analysis, gene expression analysis, and multiple sequence alignment. Servers may be used online, or the code may be downloaded.
CBIL bioWidgets for Java
[University of Pennsylvania] The bioWidgets toolkit is a collection of Java Beans ™ used for development of graphics applications and/or applets in thegenomics domain.
[Technelysium] This program displays and prints chromatogram files from ABI automated DNA sequencers and Staden SCF files, and it allows the user to manipulate the sequences.
[Univ. College London] Cinema allows the building of alignments interactively; either by using a free-format Cut and Paste facility to import a protein or DNA sequence, or by adding sequences directly from the OWL composite database. Alternatively, alignments may be loaded from the PRINTS fingerprint database and again may be customized by the addition of user-defined or OWL sequences.
Computational Biology and Informatics Laboratory
[University of Pennsylvania] Multiple bioinformatics related tools and databases. The site also includes information about related degree programs and UPenn.
Computational Biology Tools
[Cornell Theory Center] This site provides several downloadable programs for analyzing protein sequences for predictions in the areas of folding, structure determination, energetics, and dynamics. It also is home to the LOOPP program (Learning, Observing and Outputting Protein Patterns), a program for potential optimization and alignments. LOOPP aligns sequence to sequence, sequence to structure, and structure to structure.
[GSF] Predicts potential binding sites in sequences of unlimited length by comparing candidates with predefined consensus descriptions of protein binding sites. These consensus descriptions produced by the program ConsInd consist of the length of the binding site and the individual conservation of each nucleotide position within the site.
Cornell Theory Center
[Advance Cluster Computing Consortium] A high-performance computing and interdisciplinary research center. This site provides information about the center, resources like software and training, and research information.
DARWIN Molecular Sequence Analysis
[CBRG] An interactive tool for peptide and nucleotide sequence analysis with a library of functions for sequence management and analysis, statistics, numerics, and graphics.
DDL – Drug Design Laboratory
[Milan University, Italy] This site presents downloadable programs for drug design, including molecular dynamics for solvated molecules, program Predator to predict secondary structure of proteins, and molecular orbital calculations.
[GSF] DIALIGN is a novel program for multiple alignment. It constructs pairwiseand multiple alignments by comparing whole segments of the sequences. No gap penalty is used. This approach isespecially efficient where sequences are not globally related but share only local similarities, as is the case withgenomic DNA and with many protein families.
[Carlsberg Laboratory] Software for handling and analysis of nucleotide and protein sequences. This downloadable package also has special functions for EST and SAGE handling and analysis.