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2nd Window Opens resource in a 2nd browser window.

2nd Window 101science.com
Mircobiology Software. 101science.com is a science web directory, tutor, and research learning center.
[more info][13501]

2nd Window A. C. R. Martin Bioinfo Site
Downloadable Java software for bioinformatics, including a Needleman-Wunsch program and a protein structural least-squares fit program.
[more info][13719]

2nd Window ALSCRIPT
[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."
[more info][12176]

2nd Window 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.
[more info][11235]

2nd Window AMPS
[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.
[more info][11148]

2nd Window 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.
[more info][12372]

2nd Window Aneda
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.
[more info][13763]

2nd Window ANTHEPROT
[Institute of Biology and Chemistry of Proteins] (ANalyse THE PROTeins) This free software application integrates into a single package most of the methods designed for protein 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, and titration curve.
[more info][11236]

2nd Window 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.
[more info][13728]

2nd Window 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.
[more info][13639]

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2nd Window BandScan
[Glyko] Protein gel image acquisition, documentation, and analysis.
[more info][11237]

2nd Window BASS
[Whitehead Institute for Biomedical Research] A software program for tracking, extracting, and base calling DNA sequencing gels.
[more info][11238]

2nd Window BioCatalog
[EMBL] The Biocatalog is a software directory of general interest in molecular biology and genetics. The full database is downloadable (text file).
[more info][12399]

2nd Window Biocompare
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 information about the latest technologies in the life science community and provides scientists with a list of companies that offer discounts for setting up new laboratories.
[more info][10137]

2nd Window 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.
[more info][12148]

2nd Window BLOCK
[Aalborg University] This Blocking Gibbs Sampling for Pedigree (Linkage) Analysis in Very Large Pedigrees program is for linkage analysis of large complex pedigrees.
[more info][11151]

2nd Window BOXSHADE
[EMBnet.ch+] A program that uses preprocessed multiple alignment files as input to produce printouts of aligned protein or DNA sequences.
[more info][11239]

2nd Window CBIL bioWidgets for Java
[University of Pennsylvania] The bioWidgets toolkit is a collection of Java Beans (tm) used for development of graphics applications and/or applets in the genomics domain.
[more info][12405]

2nd Window Chime
[Univ. of Massachusetts, Department of Microbiology] This program is used to view molecular structures on Netscape.
[more info][11293]

2nd Window Chromas1.2
[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.
[more info][11240]

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2nd Window CINEMA
[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.
[more info][10386]

2nd Window CLUSTAL W
[SGI] This is a multiple sequence alignment program for biological sequences.
[more info][11153]

2nd Window ClustalW
[EBI] ClustalW is a popular and improved multiple alignment program for DNA or proteins.
[more info][11242]

2nd Window 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.
[more info][12053]

2nd Window 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.
[more info][12374]

2nd Window ConsInspector
[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.
[more info][11243]

2nd Window Coresearch
[GSF] This program is used to identify and delimitate consensus elements (e.g. protein binding sites) in a set of unaligned nucleic acid sequences.
[more info][11244]

2nd Window 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.
[more info][12491]

2nd Window 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.
[more info][12065]

2nd Window 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.
[more info][13641]

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2nd Window Decodon
[Decodon] Analyze protein 2-dimensional gels. Compare protein spots on two gels with image analysis techniques. Download free demo version or purchase full program.
[more info][13609]

2nd Window Delila
[National Cancer Institute] This software is for information analysis of protein and nucleic-acid sequences.
[more info][11246]

2nd Window DIALIGN
[GSF] DIALIGN is a novel program for multiple alignment. It constructs pairwise and multiple alignments by comparing whole segments of the sequences. No gap penalty is used. This approach is especially efficient where sequences are not globally related but share only local similarities, as is the case with genomic DNA and with many protein families.
[more info][11247]

2nd Window DNAssist
[DNAssist] A DNA sequence editing and analysis application.
[more info][12407]

2nd Window DNATools
[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.
[more info][11249]

2nd Window DomainFinder 1.0
[K. Hinsen] (Centre National de la Recherche Scientifique) A program for the determination and characterization of dynamical domains in proteins.
[more info][11218]

2nd Window Dotter
[Karolinska Institutet, Center for Genomics Research] Compares two related sequences and finds matches, creating a dotplot. Accompanying the dotplot are excellent statistics and user-friendly adjustment of thresholds. Download the program to run on Unix. A server version is available at http://www.hgmp.mrc.ac.uk/Registered/Option/dotter.html for registered users.
[more info][13604]

2nd Window DSSP Source Code
[CMBI] "The DSSP database is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB)."
[more info][12258]

2nd Window EBI ftp Server
The EBI ftp server provides a comprehensive archive of databases and software in the field of bioinformatics.
[more info][12395]

2nd Window FAKtory
[Arizona Research Laboratories] FAKtory is a software environment for supporting DNA sequencing projects. FAKtory runs on machines configured with the UNIX operating system. It is called FAKtory because it employs our FAKII Fragment Assembly Kernel that is a C-library of routines incorporating our best algorithms for solving the shotgun assembly problem. FAKtory is highly configurable and can perform fragment clipping, prescreening, and tagging functions, shotgun assembly with or without constraints, and sequence finishing. An extensible input/output mechanism permits FAKtory to be inserted into any informatics environment.
[more info][11764]

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2nd Window FASTA Program ftp
[University of Virginia] The latest versions of the FASTA sequence similarity search programs are available for download at this site.
[more info][12137]

2nd Window Flip
[Univ. Montreal] A Unix C program used to find and translate ORFs. Flip reformats DNA sequences, and produces output files that can be used by other programs such as FASTA.
[more info][11159]

2nd Window FramePlus
[Compugen] An algorithm for searching protein databases with DNA queries, based on Smith-Waterman. FramePlus independently and simultaneously models frame shifts and codon gaps.
[more info][12064]

2nd Window FSSP ftp Site
[EBI] The FSSP database is based on exhaustive all-against-all 3D structure comparison of protein structures currently in the Protein Data Bank (PDB).
[more info][12240]

2nd Window Garlic Software
[University of Split, Croatia] A free molecular visualization program intended to ease some of the hardships non-computer scientists may have with RasMol's command line interface.
[more info][12354]

2nd Window Geanfammer
[Medical Research Council, UK] A program for the analysis of bacterial genomes.
[more info][11251]

2nd Window GelReader
[NCSA] A color imaging and analysis tool that extracts information from digitized electrophoretic gel images, allowing manipulation of lanes and bands.
[more info][11252]

2nd Window Genalysis
[GenPak Inc.] Compare whole genomes at the DNA sequence level, looking for identical stretches of bases. Program creates a dotplot, sequence list, and statistics. Download a working version free, or pay for the expensive version.
[more info][13590]

2nd Window GeneDoc
[Pittsburgh Supercomputing Center] GeneDoc does sequence alignment editing and shading, as well as secondary structure shading and super family group support.
[more info][11253]

[MIT] A software package that allows the very rapid extraction of complete multipoint inheritance information from pedigrees of moderate size. This information is then used in exact computation of multipoint LOD scores and in a new method of non-parametric linkage analysis.
[more info][11162]

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2nd Window Genemachine
[J. Ryan, NHGRI] Runs GRAIL, MZEF, GENSCAN, FGENES, Sputnik, RepeatMasker, and BLAST; and prints the output in ASN.1 format.
[more info][11391]

2nd Window GeneMark
[Georgia Tech] This program is used for gene prediction in sequences. "The GeneMark program relies upon an Inhomogeneous Markov Model approach combined with training datasets to predict genes. Along with predicting genes, it can use RBS models to predict RBS sites and predict frameshifts."
[more info][11163]

2nd Window Genetics Software Archive
[Indiana State Univ.] Annotated links to downloadable genetics and molecular biology software for the PC.
[more info][12401]

2nd Window Genome Inspector
[GSF] This software tool detects distance associations between sequence elements.
[more info][11164]

2nd Window Getlanes
[Washington School of Medicine] Software developed to track lanes in four-color, flourescence-based, electrophoretic gel images for use in large scale sequencing projects.
[more info][11254]

2nd Window GLIMMER
[TIGR] "Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria and archaea. Glimmer (Gene Locator and Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA."
[more info][12035]

2nd Window GRASP Software
[Columbia University] "GRASP is a molecular visualization and analysis program. It is particularly useful for the display and manipulation of the surfaces of molecules and their electrostatic properties."
[more info][12348]

2nd Window HMMER 2.1.1
[Washington Univ., St. Louis] A protein sequence analysis tool that profiles hidden Markov models (profile HMMs) that can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus.
[more info][10452]

2nd Window HMMpro
[Net-ID, Inc.] A general purpose hidden Markov model (HMM) simulator for biological sequence analysis.
[more info][12215]

2nd Window ICM
[Molecular Software] Molecular visualization software with an easy to use GUI.
[more info][12345]

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2nd Window ITERALIGNv1.1
[Stanford University] (Luciano Brocchieri) A program for the multiple alignment of protein sequences.
[more info][12166]

2nd Window JamBW 1.1: Java Based Molecular Biologist's Workbench
[EMBL] A collection of programs designed to exploit the most common bioinformatic operations that a molecular biologist currently has, including manipulation and analysis of DNA sequences.
[more info][11167]

2nd Window JOY Software
[University of Cambridge] JOY is a program to annotate protein sequence alignments with three-dimensional (3D) structural features.
[more info][12310]

2nd Window Kinemage
[D. Richardson, Duke Univ.] A package of 2 programs, Prekins and Mage, that enables the user to create a 3-D image from a PDB-format coordinate file, which then can be modified.
[more info][11305]

2nd Window LalnView
[PBIL] A graphical program for visualizing local alignments between two sequences for proteins and nucleic acids.
[more info][11257]

2nd Window Links to molbio software
[Erasmus University] Annotated links to downloadable molecular biology software.
[more info][12402]

2nd Window Linux for Chemists
A virtual library of Linux software links in the areas of chemistry, biochemistry, computational biology and bioinformatics.
[more info][13754]

2nd Window MACAW ftp Site
[NCBI] "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."
[more info][12170]

2nd Window MacStripe
[Univ. of York] MacStripe will explore potential alpha-helical coiled coils in the sequence of a protein.
[more info][11259]

2nd Window MatInd and MatInspector2.1
[GSF] Tools for detection of consensus matches in nucleotide sequence data .
[more info][11260]

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2nd Window MegaPOV
[Nathan Kopp] [Annotation pending]
[more info][12318]

2nd Window MICE
[San Diego Supercomputing Center] "The MICE application provides high quality, interactive visualization of molecular scenes. Written in JavaTM and Java3D, MICE is designed according to the Java philosophy of “write once, run anywhere.” Portable and web-deliverable, the MICE application enables users to not only view molecular scenes on their own computer, but to distribute these scenes and interact with other users anywhere on the internet."
[more info][12352]

2nd Window The Microbiology Network
Molecular Biology and Biotechnology File Archive. These files include standard shareware programs of interest to the microbiologist, programs designed by individual investigators, text files in specialized interest, and demonstration programs supplied by vendors.
[more info][11248]

2nd Window ModelGenerator & ModelInspector
[GSF] Methods for generation and recognition of models for regulatory regions in DNA sequences.
[more info][11262]

2nd Window MODELLER
[Rockefeller Univ.] A program for homology protein structure modelling by satisfaction of spatial restraints.
[more info][11224]

2nd Window Molecular Biology Software
[Hospital for Sick Children, Toronto] Perl source code programs for DNA sequence analysis and other bioinformatics related applications.
[more info][11155]

2nd Window Molecular Structure Computer Programs
[University of Lunds] Several program packages dealing with molecular structure analysis and NMR data analysis.
[more info][12299]

2nd Window MOLMOL 2.4
This is a program for the analysis and display of molecules.
[more info][11315]

2nd Window MolPOV Software
[University of Florida] "A PDB to POV file converter and molecular visualization tool for MS Windows."
[more info][12347]

2nd Window MolScript Software
[Avatar Software AB] "MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations."
[more info][12344]

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2nd Window MPSA
[NPSA] "Multiple Protein Sequence Analysis is a stand-alone software package for protein sequence analysis with a high integration level and Web client/server capabilities. It provides many methods and tools, which are integrated into an interactive graphical user interface."
[more info][11263]

2nd Window MSA
[Rice Univ.] A program to do multiple sequence alignment under the sum-of-parts criterion.
[more info][11170]

2nd Window MSA: Multiple Sequence Alignment
[Washington Univ.] Reads a file containing several protein sequences and attempts to produce a multiple alignment of these sequences, which it will write to standard output. MSA uses the algorithm of Altshcul et al., Gupta et al. or ClustalW.
[more info][10458]

2nd Window MView
[National Institute for Medical Research] Converts the results of BLAST, FASTA, and other sequence database searches to a coloured multiple alignment of hits stacked against the query.
[more info][12135]

2nd Window Naccess
[S. Hubbard & J. Thornton, UMIST] A stand alone program that calculates the accessible area of a molecule from a PDB format file. It can calculate the atomic and residual accessiblities for both proteins and nucleic acids.
[more info][11114]

2nd Window NCBI FTP Site
Provides FTP access to NCBI tools and databases, including BLAST, Cn3D, Sequin, the NCBI Toolbox, BLAST databases, GenBank, and many collections of contributed molecular biology data.
[more info][12393]

2nd Window Noncovalent Bond Finder
[University of Massachusetts] [Annotation pending]
[more info][12337]

2nd Window Nucleic Acid Structure Analysis
[International Union of Crystallography] This program calculates all of the rotational and translational parameters for complementary base pairs, neighboring base pairs in Cartesian and helical coordinate frames, and base to base Cartesian and helical parameters along each strand.
[more info][11267]

2nd Window Octopus
[Laboratoire de Minéralogie-Cristallographie] (Patrick Durand) Octopus is an interactive program designed for the rapid interpretation of BLAST, BLAST-2, and FASTA output text files. It provides an easy-to-use graphical user interface for both experienced and inexperienced users with sequence comparison analysis based on the widely-used BLAST series of softwares.
[more info][12404]

2nd Window ORBIT
[Murdoch University] The Online Researchers Bioinformatics Interface Tools project was established to implement an easy to use web based interface for registered members of the Murdoch Bioinformatics Research Group (MBRG). The system provides interfaces to the server side programs BLAST, Repeat Masker, and ClustalW; while still providing a framework for many other programs to be added to the interface in the future. This is a downloaded Java program.
[more info][12406]

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2nd Window PASSML
[University of Cambridge] A program for infering phylogeny of globular proteins.
[more info][12184]

2nd Window Patched POV-ray Version
[Biozentrum, University of Basel] A patch to the current (3.1g) POV-ray source which adds the object smooth_color_triangle to a mesh object. This allows for triangles with individual colors for each vertex, which are interpolated during rendering.
[more info][12319]

2nd Window pDRAW32 DNA analysis software
[AcaClone Software] A free, feature-rich, DNA software application. Capabilities include annotation, cloning, sequence editing, enzyme selection, graphical output, and more. According to the author, "Actually pDRAW32 is not freeware - rather it is "beerware." This means that if you like the program you are encouraged to buy me a beer if you should meet me at a scientific meeting. You are mostly at risk of that if you attend conferences on yeast genetics."
[more info][12076]

2nd Window Pfam ftp Site
[Washington University, St. Louis] The ftp site for downloading the Pfam protein domain database and the associated tools.
[more info][12196]

2nd Window PHD Secondary Structure Software ftp Site
[Columbia University] [Annotation pending]
[more info][12265]

2nd Window Phred Phrap Consed System Home Page
[University of Washington] This set of widely used programs does the following. Phred reads DNA sequencer trace data, calls bases, and assigns quality values to the bases. Phrap assembles shotgun DNA sequence data. Consed is graphical tool for editing Phrap assemblies. SWAT and CROSS_MATCH do sequence similarity searches.
[more info][13444]

2nd Window Phylogeny Programs
[University of Washington] A list of over 100 phylogeny software packages.
[more info][11375]

2nd Window Pratt - A Pattern Discovery Tool
[University of Bergen] Discovers patterns conserved in sets of unaligned protein sequences.
[more info][11272]

2nd Window Pred2ary
[University of California, San Francisco] A service for protein secondary structure and class prediction.
[more info][12278]

2nd Window PREDATOR
[EMBL] Protein secondary structure prediction from a single sequence or a set of sequences.
[more info][10508]

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2nd Window PredictProtein Server
[EMBL] Permits the user to submit a sequence for prediction. Links to other pages for multiple sequence alignment, prediction of secondary structure, prediction of solvent accessibility, prediction of transmembrane helices, prediction of topology for transmembrane proteins, fold recognition by prediction-based threading, and evaluation of secondary structure prediction accuracy.
[more info][10509]

2nd Window PROBE ftp Site
[NCBI] PROBE is a tool for extraction of multiple alignments from a sequence database.
[more info][12165]

2nd Window Programs for biosequence analysis
This page contains example implementations in Java of some algorithms for pairwise alignment (including the Needleman-Wunsch algorithm), hidden Markov models (HMMs), and phylogenetic trees. Some are available as Java applets you can run from this page.
[more info][10370]

2nd Window Promotif
[Univ. College London] Analyzes a protein coordinate file and provides details of the structural motifs in the protein.
[more info][11273]

2nd Window PROMOTIF Software
[University College London] "Promotif analyzes a protein coordinate file and provides details of the structural motifs in the protein."
[more info][12302]

2nd Window ProMSED2 and ViSEd1.1 ftp Site
[Indiana University] At this ftp site, users may download ProMSED2 and ViSEd1.1 which are both muliple sequence alignment editors for the Windows platform.
[more info][12171]

2nd Window Protein Analysis & Modelling Software
[University College London] Publicly available bioinformatics software. Most of these programs are for the analysis of protein sequence and structure.
[more info][12301]

2nd Window Protein Modeling Software and Services
[University of California, San Francisco] Access to protein modeling programs produced in the Fred Cohen Laboratory.
[more info][12253]

2nd Window Protein Modelling Software
[National University of Singapore] Well-annotated links to software for protein modelling programs and their online manuals.
[more info][12311]

2nd Window P-SEA Software
[Centre de Biochimie Structurale] This new software assigns secondary structure elements in protein structures from the Ca trace (Labesse G., Colloc'h N., Pothier J. and Mornon J.-P., CABIOS, vol 13., no. 3, pages 291-295).
[more info][12274]

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2nd Window RasMol 2.7.1 and 2.7.2
[Bernstein+Sons] New versions of RasMol, for molecular display and manipulation, with new manual, languages other than English.
[more info][13614]

2nd Window RasMol, Chime & Protein Explorer
[University of Massachusetts] [Annotation pending]
[more info][12322]

2nd Window RBSfinder
[TIGR] RBSfinder is a Perl script that implements an algorithm to find ribosome binding sites for genes in bacterial and archaeal genomes. It is normally run as a post-processor to the Glimmer gene finder or to other prokaryotic gene finders.
[more info][14109]

2nd Window Restriction Map Alignment
[USC Computational Biology] This program reads restriction maps and deciphers alignments using a quantic map alignment algorithm.
[more info][11275]

2nd Window Retrak v1.5
[Washington Univ. - St. Louis] A retracking and analysis environment for processing a large volume of gel samples.
[more info][11276]

2nd Window ReView
[Gosper, Brunel Univ.] This program is a 4-D chemical viewer/analyzer, which is capable of 3-D molecular display, animation, and geometrical analysis.
[more info][11338]

2nd Window SAGA
[Centre National de la Recherche Scientifique] Sequence Alignment by Genetic Algorithm. SAGA is optimally designed for the alignment of less than 20 sequences and less than 400 residues.
[more info][12164]

2nd Window Saturated BLAST
An automated multiple intermediate sequence search used to detect distant sequence homology. Intermediate sequence search is a strategy for recognizing distant homologues using transitive sequences. This method is useful when similarity between two remotely homologous sequences can not be detected by normal sequence comparison.
[more info][13760]

2nd Window SC rate
[MRC Laboratory of Molecular Biology] A Perl5 program that evaluates the accuracy of protein sequence alignments with very low sequence identity.
[more info][11278]

2nd Window SCANPS
[EBI] A local alignment method to search protein sequence databases with a query sequence or multiple alignment, and also allows all pairwise comparisons to be made between a set of sequences and can estimate the statistical significance of the alignments.
[more info][11174]

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2nd Window SEALS
[NCBI] A software package expressly designed for large-scale research projects in bioinformatics. Its goal is "to facilitate large-scale semi-automatic sequence analysis projects, leveraging human intelligence by simplifying laborious tasks, without taking human judgment out of the loop."
[more info][11279]

2nd Window SeaView
[Genetique et Biologie des Populations] This is a multiple sequence alignment editor.
[more info][11280]

2nd Window See in 3-D
[NCBI] (Cn3D) "Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service."
[more info][12340]

2nd Window SeqPup
[Indiana Univ.] A biosequence sequence editor and analysis program for multiple sequence alignments and single sequence editing.
[more info][11281]

2nd Window Simple34
[Australian National Univ.] This program estimates the amount of local sequence repetition in nucleotide sequences.
[more info][11283]

2nd Window Software Tools
[TIGR] A list of links to very useful molecular biology and bioinformatics-related freeware. The list includes programs for DNA sequencing and sequence analysis, genomic searches, and microarray image processing.
[more info][12051]

2nd Window SSS Align
[Univ. of Edinburgh] A software implementation of the Smith/Waterman best local similarity algorithm which, in addition to the traditional Dayhoff PAM scoring scheme, has the ability to use secondary structure prediction in order to align sequences which have identities as low as 15% and still identify those sequences as significant.
[more info][11284]

2nd Window STAMP
[The Barton Group] A suite of programs for the comparison and alignment of protein three dimensional structures. The suite will multiply align structures and produce a corresponding sequence alignment with confidence values associated with each aligned position.
[more info][11231]

2nd Window STAMP
[EBI] "STAMP is a package for the alignment of protein sequence based on three-dimensional (3D) structure. It provides not only multiple alignments and the corresponding `best-fit' superimpositions, but also a systematic and reproducible method for assessing the quality of such alignments."
[more info][12222]

2nd Window STING Server and Software
[Weizmann Institute] "STING is a WWW tool for the simultaneous display of information about macromolecular structure (in STING's Graphics Frame) and sequence (in STING's Sequence Frame). Special attention is given to MacroMolecular INTERFACE analysis."
[more info][12342]

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2nd Window STRIDE Documentation
[EMBL] STRIDE provides knowledge-based protein secondary structure assignment from atomic coordinates.
[more info][12256]

2nd Window Swiss-PdbViewer
[ExPASy] Provides an interface allowing analysis of several proteins at the same time by superimposing them in order to deduce structural alignments and compare their active sites or any other relevant parts.
[more info][12341]

2nd Window TeXshade
[University of Tuebingen] "TeXshade is an alignment shading software completely written in TeX/LaTeX which can process multiple sequence alignments in the .MSF and the .ALN file format. It provides in addition to common shading algorithms special shading modes featuring functional aspects, e.g. charge or hydropathy, and a plenitude of commands for handling shading colors, text styles, labels, legends and even allows the user to define completely new shading modes."
[more info][12179]

2nd Window vExplorer
[Future Skill software] This is a metabolic control analysis tool.
[more info][11396]

2nd Window VMD Software
[University of Illinois at Urbana-Champaign] Visual Molecular Display "is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running Unix or Windows, is distributed free of charge, and includes source code."
[more info][12350]

2nd Window Webblast
[Hospital for Sick Children, Toronto] A perl program that conducts NCBI blast searches by acting as a WWW client like Netscape or Internet Explorer. The program saves results as local files in HTML or plain text.
[more info][11285]

2nd Window WebBLAST
[National Human Genome Research Institute] NHGRI WebBLAST is a suite of downloadable software tools to aid in viewing and organizing genetic sequencing data.
[more info][11993]

2nd Window WHAT IF
[CMBI] This protein structure analysis program can be used for molecular graphics and structure verification.
[more info][11352]

2nd Window Wise2
[Sanger Center] A software package that compares DNA sequences at the level of conceptual translation, regardless of sequencing error and introns. It can compare a single protein or a profile HMM to a genomic DNA sequence, and predict a gene structure.
[more info][11287]

2nd Window WPDB
[San Diego Supercomputing Center] "The PDB through Microsoft Windows, or WPDB for short, is a Microsoft Windows 3.1, Windows95, and Windows NT (client and server) based program to interrogate the 3-dimensional structure of biological macromolecules as found in the Protein Data Bank (PDB) using query and display tools like those shown above. "
[more info][12358]

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2nd Window WU-BLAST
[Washington Univ., St. Louis] This is software for gene and protein identification through sensitive, selective, and rapid similarity searches of protein and nucleotide sequence databases.
[more info][11288]

2nd Window X-PLOR
[Yale] This program has files for protein and DNA/RNA X-ray crystallography and solution NNR spectroscopy.
[more info][11397]

2nd Window XYLEM
[University of Manitoba] A collection of tools designed enable the user to identify, extract, and manipulate data from major databases such as GenBank, EMBL and PIR.
[more info][11289]

2nd Window YASARA Software
[University of Graz] "YASARA is an interactive real-time molecular dynamics program, covering various topics in the field of molecular modeling, protein fold calculation (based on NMR data), tertiary structure prediction, protein / DNA docking, and parallel macromolecular dynamics."
[more info][12351]


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