| Structural Biology Calculations
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A tool for calculating geometric quantities of proteins (accessible surface area, volume, etc).
Submitted Oct 19, 2000
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| Compute pI/Mw
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Compute pI/Mw is a tool which allows the computation of the theoretical pI (isoelectric point) and Mw (molecular weight) for a list of SWISS-PROT and/or TrEMBL entries or for a user entered sequence.
Submitted Oct 22, 2000
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| PredictProtein
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PredictProtein is a service for sequence analysis, and structure prediction. It does You submit any protein sequence. PredictProtein retrieves similar sequences in the database and predicts aspects of protein structure.
Submitted Oct 19, 2000
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| CpG Islands
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Utility to find CpG Islands in a user-entered sequence.
Submitted Oct 15, 2000
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| Eukaryotic Promoter Database
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The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references.
Submitted Nov 19, 2000
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| Scanps 2.3
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A fast implementation of the true Smith & Waterman algorithm for protein database searches.
Submitted Oct 22, 2000
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| ParAlign
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You may search a number of sequence databases for sequences similar to your amino acid query sequence using two very sensitive algorithms. You can choose between a fast implementation of the well-known Smith-Waterman optimal local alignment algorithm or a new algorithm called ParAlign, which is much faster but still almost as sensitive. Both algorithms are implemented using bit-parallelism on a single Pentium III microprocessor, exploiting the MMX and SSE instruction sets. The current implementation of the affine Smith-Waterman algorithm has a speed of about 220 million cells per second (on a 500MHz CPU), which is a nine-fold speed-up relative to SSEARCH.
Submitted Nov 18, 2000
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| ProtParam
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ProtParam is a tool which allows the computation of various physical and chemical parameters for a given protein stored in SWISS-PROT or TrEMBL or for a user entered sequence. The computed parameters include the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY).
Submitted Oct 22, 2000
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| SYSTERS Cluster Set
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SYSTERS (SYSTEmatic Re-Searching) is based on iterative calls of a traditional database search tool like BLASTP or FASTA. The searching algorithm explores the sequence space around a query sequence - called seed - and finds a set of related sequences to this seed - called cluster - which share a strong similarity. The sequences within a cluster are not ranked - a sequence is either in the cluster or it is not. To circumvent problems originating in asymmetric search results, for each pair of sequences identified by a database search a local alignment is computed using LALIGN and a symmetric E-value is recomputed.
Submitted Nov 18, 2000
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| BioInfo.PL Meta Server
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The Structure Prediction Meta Server offers a single gateway to various structure prediction tools. The user can submit an amino acid sequence as input. The sequence will be first analysed for close homologs in the Protein Data Bank, using Blast. If no close homologs (cutoff 0.1) are detected the sequence will be submitted to the structure prediction servers. The results of the prediction will be stored localy.
Submitted Sep 26, 2000
Updated Apr 30, 2008
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| Cleaner
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Online cleaning tool for DNA/RNA or protein sequences. Very useful! It removes all unwanted characters and comments from sequences. Ideal for database retrieved sequences.
Submitted Mar 10, 2003
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| dnadist
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Program to compute distance matrix from nucleotide sequences.
Submitted Oct 25, 2000
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| Edinburgh Biocomputing Systems Limited
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EBS, a spin out company from the University of Edinburgh
formed to develop and market MPSRCH. The software, which implements the full Smith and Waterman algorithm on reasonably priced general purpose hardware, can be accessed free of charge upon registration at the site.
Submitted Sep 26, 2000
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| GlycoMod
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GlycoMod is a tool that can predict the possible oligosaccharide structures that occur on proteins from their experimentally determined masses. The program can be used for free or derivatized oligosaccharides and for glycopeptides.
Submitted Dec 18, 2000
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| ISREC PatternFind
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This server allows you to search the nonredundant or SwissProt protein database with a user-defined pattern. The pattern can either be a PERL-supported regular expression or a pattern in PROSITE format. The output is either a report on the matches, a multiple sequence file containing all matching patterns (in Pearson format), or a multiple sequence file containing all matching pattern instances.
Submitted Dec 02, 2000
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| Multalin
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Graphical version for alignment of multiple sequences using the MultAlin algorithm.
Submitted Oct 20, 2000
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| NIX
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NIX is a WWW tool to view the results of running many DNA analysis programs on your DNA sequence.
Submitted Sep 26, 2000
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| Pyramids
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A pyramidal analysis tool for sequence clustering (JC AUDE).
Submitted Nov 24, 2000
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| SeqPainter
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Online painter tool to colorize protein residues according to user defined parameters. Very simple and quick!
Submitted Mar 10, 2003
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| SIM Alignment Tool
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SIM is a program which finds a user-defined number of best non-intersecting alignments between two protein sequences or within a sequence.
Submitted Oct 20, 2000
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| 2DWG Image Meta-Database
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The 2DWG meta-database of 2D-PAGE protein gel images found on the Web. A meta-database contains information about data in other databases. The 2DWG database is a organized as a spreadsheet table with each gel image represented by a row. Data for each gel entry includes tissue, species, cell-line, image URL, database URL, gel protocol, organization URL, image properties, map URL if it exists, etc. It uses a simple database search engine dbEngine to access selected rows of gels in the full 2DWG table.
Submitted Dec 03, 2000
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| 3D-PSSM
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A Fast, Web-based Method for Protein Fold Recognition using 1D and 3D Sequence Profiles coupled with Secondary Structure and Solvation Potential Information.
Submitted Oct 15, 2000
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| AGADIR
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An algorithm to predict the helical content of peptides.
Submitted Oct 22, 2000
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| DAS
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The DAS server will predict transmembrane regions of a query sequence. Enter your query protein sequence into the text area below and submit it to the server. The sequence should be in one letter code.
Submitted Oct 19, 2000
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| GeneStream II
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Sequence comparision and search programs, including the rigorous Smith-Waterman algorithm (in FastA and Ssearch).
Submitted Nov 10, 2000
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| IMAGEne
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All sequence from I.M.A.G.E. human cDNA clones have been used to create two types of gene clusters: Known Gene Clusters based on NCBI's Reference Genes, and Candidate Gene Clusters having no known gene association. TIGR clones are used to supplement the Candidate Gene clustering. Those clones whose sequence does not match any other cDNA are grouped as Singletons. Submit a query against either cluster set to obtain a ranked display of available I.M.A.G.E. clones aligned with the corresponding known human gene or consensus sequence.
Submitted Nov 18, 2000
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| MaxSprout
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MaxSprout is a fast database algorithm for generating protein backbone and side chain co-ordinates from a C(alpha) trace. The backbone is assembled from fragments taken from known structures. Side chain conformations are optimized in rotamer space using a rough potential energy function to avoid clashes.
Submitted Oct 08, 2000
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| MULTIDOCK
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The program MULTIDOCK was developed to provide a method for refining the interface between two proteins at the atomic level given an initial docked complex generated by a docking algorithm or manual docking procedure. The motivation for this work was to provide a rapid energy refinement protocol for the large number of putative docked complexes produced by rigid-body docking programs such as FTDOCK or DOCK. The program models the effects of side-chain conformational change and the rigid-body movement of the interacting proteins during refinement.
Submitted Dec 09, 2000
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| NetChop
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The NetChop WWW server produces neural network predictions for cleavage sites of the human proteasome.
Submitted Dec 02, 2000
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| ORFViewer
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ORF detection and prediction tool. Represents graphically the ORFs on DNA sequence in 6 reading phases.
Submitted Mar 10, 2003
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| PeptideMass
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PeptideMass cleaves one or more protein sequences from the SWISS-PROT and/or TrEMBL databases or a user-entered protein sequence with a chosen enzyme, and computes the masses of the generated peptides. The tool also returns theoretical isoelectric point and mass values for the proteins of interest. If desired, PeptideMass can return the mass of peptides known to carry posttranslational modifications, and can highlight peptides whose masses may be affected by database conflicts, isoforms or splicing variants.
Submitted Oct 22, 2000
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| PhosphoBase
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PhosphoBase is a revised database of phosphorylation sites in proteins. Information about the position of phosphorylated serines, threonines, or tyrosines and relevant kinetic parameters are presented.
Submitted Oct 22, 2000
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| Phosphoprotein Database (PPDB)
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The purpose of a Phosphoprotein Database (PPDB) is to promote a systematic approach to the study of cellular protein phosphorylation. PPDBs have the potential to transform 2DE images from mere collections of spots on gels into images that convey information about cell lineage, the activation state of the cell, the ligands that the cell has encountered, the kinases, phosphatases and substrates present in the cell, and the activation state of these enzymes.
Submitted Nov 19, 2000
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| PIX
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PIX is a WWW tool to view the results of running many peptide analysis programs on your peptide sequence.
Submitted Sep 26, 2000
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| Protein Domain Profile Analysis
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This tool allows you to search our library of functional diagnostic profiles with a protein sequence. A match to one or more of these profiles provides you with an effective multi-alignment of your query sequence to the best-matched profile's defining set of proteins along with its annotations. This in turn allows one to propose that the matching sequence contains a domain of similar structure and function.
Submitted Oct 22, 2000
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| PSA Structure Prediction
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The Protein Sequence Analysis (PSA) server predicts probable secondary structures and folding classes for a given amino acid sequence.
Submitted Oct 22, 2000
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| Quick Protein Translator
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Translate DNA sequences in all 6 reading frames.
Submitted Oct 15, 2000
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| SDSC Biology Workbench
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The Biology WorkBench is a revolutionary web-based tool for biologists. The WorkBench allows biologists to search many popular protein and nucleic acid sequence databases. Database searching is integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems.
Submitted Sep 26, 2000
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| SSCP
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The program SSCP computes predictions for the content of helix, strand, and coil for a given protein using the amino acid composition as the only input information. The basic idea of the method consists in the application of analytic vector decomposition methods applied on the composition vector of the query protein. Both sequences and composition data are allowed as program input.
Submitted Oct 22, 2000
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| TMAP
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TMAP multiple sequence alignment form.
Submitted Oct 08, 2000
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| TMpred
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The TMpred program makes a prediction of membrane-spanning regions and their orientation. The algorithm is based on the statistical analysis of TMbase, a database of naturally occuring transmembrane proteins. The prediction is made using a combination of several weight-matrices for scoring.
Submitted Oct 22, 2000
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| Web Cutter Tool
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Web Cutter tool, to analyse DNA sequences restriction sites.
Submitted Mar 10, 2003
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| Yale Molecular Biophysics Biochemistry Center Structural Biology
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User Guides and worked examples for software applications in structural biology
Submitted Nov 05, 2000
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| AbCheck
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This page allows you to test an antibody sequence against the Kabat sequence database. Any unusual residues (occurring in < 1% of chains in the database) will be reported to you. This allows the identification of potential cloning artifacts and sequencing errors.
Submitted Oct 24, 2000
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| AMAS Server
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This server allows you to run AMAS on your own multiple sequence alignment.
Submitted Oct 08, 2000
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| BLOCK Maker
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The BLOCK MAKER SERVER finds blocks in a group of related protein sequences. Blocks are short multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins. Typically, a group of proteins has more than one region in common and their relationship is represented as a series of blocks separated by unaligned regions.
Submitted Nov 18, 2000
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| BLOCKS
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Blocks are short multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins. As an aid to detection and verification of protein sequence homology, the BLOCKS e-mail searcher compares a protein or DNA sequence to the current database of protein blocks. DNA sequences are translated in all 6 frames for searching. The typical search requires only a few minutes if queries are not long DNA sequences. Answers are received by e-mail.
Submitted Oct 25, 2000
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| ChloroP
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The ChloroP WWW-server is able to predict whether or not an amino acid sequence contains an N-terminal chloroplast transit peptide, cTP and the probable site for cleavage of the transit peptide.
Submitted Oct 22, 2000
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| DARWIN
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Filling and submitting this form will execute the statements entered as a Darwin program (a tool for peptide and nucleotide sequence analysis).
Submitted Oct 25, 2000
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| DictyOGlyc
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The DictyOGlyc WWW server produces neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins.
Submitted Dec 02, 2000
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| EMBL Dali
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The Dali server is a network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank. A multiple alignment of structural neighbours is mailed back to you. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences.
Submitted Oct 08, 2000
Updated Dec 09, 2000
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| Expressed Sequence Tags
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dbEST (Expressed Sequence Tag) sequences are 'single pass' partial DNA sequences derived from clones randomly selected from cDNA libraries. dbEST is maintained by NCBI and included in the GenBank database. Because these data differ from traditional GenBank entries and thus require special processing and annotation, NCBI also makes them available in a separate database, dbEST. The full reports contain information on the availability of physical cDNA clones and mapping data in collaboration with the Genome Data Base at Johns Hopkins University.
Submitted Dec 02, 2000
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| GCG - Sequence analysis package
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This is the character interface to the GCG package. GCG is a collection of programs run in the UNIX environment for sequence analysis and manipulation.
Submitted Nov 24, 2000
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| GeneMatcher
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GeneMatcher programs and databases for your query sequence. Changing the GenMatcher parameters and output parameters is optional.
Submitted Nov 10, 2000
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| GlycanMass
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GlycanMass is a tool which allows to calculate the mass of an oligosaccharide structure.
Submitted Dec 18, 2000
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| HGMP-RC MOWSE Session
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No Description
Submitted Dec 02, 2000
Updated Dec 18, 2000
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| HIV Sequence Database
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The main aim of this website is to provide easy access to our databases, alignments, and the tools and interfaces that The HIV Sequence Database had produced.
Submitted Dec 02, 2000
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| ISREC COILS
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COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation.
Submitted Oct 22, 2000
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| ISREC ProfileScan
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This server allows you to search one or more sequences against the current release of Amos Bairochs PROSITE database. The server uses an experimental version of a PERL-script that runs a PROSITE database-search using regular expressions. The output of this server is similar to the output of the ppsearch-server running at the EBI.
Submitted Dec 02, 2000
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| LikeNess
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WWW-accessible real-time protein search & 3D-alignment using the complete PDB
Submitted Dec 01, 2000
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| MassSearch
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Search the SwissProt database for sequences which when digested by the given enzyme will match the given set of masses.
Submitted Oct 25, 2000
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| Molecular Probe Data Base (MPDB)
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The Molecular Probe Data Base (MPDB) contains information on ca. 4.300 synthetic oligonucleotides with a sequence of up to 100 nucleotides. Data are mainly taken from the literature and are encoded on the basis of controlled vocabularies.
Submitted Dec 02, 2000
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| MOWSE
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You can use these pages to submit a MOWSE database search. MOWSE will search the owl protein sequence database with protein fragment information, and return the protein(s) which most likely correspond to your peptide-data.
Submitted Dec 02, 2000
Updated Dec 18, 2000
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| mrtrans
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mrtrans is a simple program that allows you to produce aligned cDNA sequences from aligned protein sequences. This can be very useful for phylogeny programs, e.g. in PHYLIP - dnadist, dnapars, dnaml, etc. In general, it is better to use protein sequences for multiple alignments, but to use DNA sequences for phylogeny. This can be time consuming when there are gaps in the aligned protein sequences.
Submitted Nov 24, 2000
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| NetOGlyc
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The NetOglyc WWW server produces neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins.
Submitted Oct 22, 2000
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| NetPicoRNA
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The NetPicoRNA World Wide Web server produces neural network predictions of cleavage sites of picornaviral proteases.
Submitted Oct 22, 2000
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| NHGRI/NCBI Histone Sequence Database
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A comprehensive WWW resource for histones and histone fold-containing proteins.
Submitted Sep 27, 2000
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| Nnpredict
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Protein Secondary Structure Prediction.
Submitted Oct 22, 2000
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| PAPA
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Parsimony After Progressive Alignment (PAPA) Programs.
Submitted Nov 24, 2000
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| Peptide Binding Predictions
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Rank potential 8-mer, 9-mer, or 10-mer peptides based on a predicted half-time of dissociation to HLA class I molecules.
Submitted Oct 22, 2000
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| Pôle Bio-Informatique Lyonnais
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The PBIL (Pôle Bio-Informatique Lyonnais) World Wide Web server - developed at the Laboratory of Biometry and Evolutionary Biology and the Institute of Biology and Chemistry of Proteins - is dedicated to molecular biology and ecology. This server allows to browse through a number of general or specialized sequence databases such as GenBank, NBRF, EMBL, SWISS-PROT/TrEMBL, Hovergen, NRSub and EMGLib. It also allows access to many analytical tools for nucleotide or protein sequence analysis. The PBIL server also offers many documents relevant to these fields of research as well as links with other information sources.
Submitted Dec 02, 2000
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| PPSEARCH
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Scans a sequence against PROSITE (with graphical output).
Submitted Oct 22, 2000
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| PREPI
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PREPI is a molecular graphics program which can be used to EASILY produce and interactively manipulate many different types of molecular representations (cartoons) as well as providing quantative information on secondary structural topology. The program is not just limited to proteins, but can also show cartoon representations of NUCLEIC ACIDS. In fact the program is capable of displaying "ANY" object for which cartesian coordinates are available. The program can input data from a wide range of data file formats (e.g. Broohaven PDB, Cambridge Databank, SYBL, Z-MATRIX) including its own FREE FORMAT which allows for the construction of complex objects such as Virus particles.
Submitted Dec 09, 2000
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| protdist
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Program to compute distance matrix from protein sequences.
Submitted Oct 25, 2000
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| ProtScale
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ProtScale allows you to compute and represent the profile produced by any amino acid scale on a selected protein.
Submitted Oct 22, 2000
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| PSA
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The Protein Sequence Analysis (PSA) server predicts probable secondary structures and folding classes for a given amino acid sequence.
Submitted Oct 22, 2000
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| PSORT
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PSORT is a computer program for the prediction of protein localization sites in cells. It receives the information of an amino acid sequence and its source orgin, e.g., Gram-negative bacteria, as inputs. Then, it analyzes the input sequence by applying the stored rules for various sequence features of known protein sorting signals. Finally, it reports the possiblity for the input protein to be localized at each candidate site with additional information.
Submitted Oct 22, 2000
Updated Oct 31, 2000
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| RandSeq
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RandSeq is a tool which generates a random protein sequence.
Submitted Oct 22, 2000
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| SAM-T99
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HMM-based Protein Sequence Analysis, SAM-T99.
Submitted Sep 26, 2000
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| SAPS
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Statistical analysis of protein sequences.
Submitted Oct 22, 2000
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| SDSC Biology Workbench
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The WorkBench allows biologists to search many popular protein and nucleic acid sequence databases. Database searching is integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems.
Submitted Nov 10, 2000
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| SignalP
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The SignalP World Wide Web server predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks.
Submitted Oct 22, 2000
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| SMART
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SMART (Simple Modular Architecture Research Tool.) identifies and annotates domain sequences known to occur in signalling proteins.
Submitted Oct 22, 2000
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| SPIN-PP
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SPIN-PP is a database of all protein-protein interfaces present in the PDB. The program GRASP was used to create molecular surfaces of each half of all 2-chain complexes present in the PDB. A basic set of physico-chemical properties were then mapped on to these surfaces, which were then used to classify the interfaces into a surface property taxonomy. The mapped properties currently include surface curvature , electrostatic potential, based on formal charges, sequence variability , based on the HSSP alignments, and hydrophobicity ,on an atom-based model.
Submitted Oct 18, 2000
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| SRS-FastA Subset Search
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This is a service to match your query sequence against subsets of nucleic and protein databanks. These subsets are chosen by you with keyword selections in the sequence documentation.
Submitted Dec 02, 2000
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| SRSWWW at IUBio
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A list of Data Banks available at IUBio Archive, Indiana, USA.
Submitted Nov 19, 2000
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| The Nucleic Acid Database
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The goal of the Nucleic Acid Database Project is to assemble and distribute structural information about nucleic acids. Structures may be selected by making choices based on a large variety of structural and experimental characteristics. The user can then view the structure's coordinates in either NDB or PDB format, view the structure's full NDB entry, view the structure using either a local viewer or the remote viewer (RasMol), or display the structure's atlas entry.
Submitted Dec 02, 2000
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| The Protein Colourer
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A tool for colouring your amino acid sequences. The default settings will colour the sequence by the hydrophobicity of the amino acids. You can set the colouring scheme by changing the lists associated with each colour. Another scheme could be used to colour the amino acids by size.
Submitted Oct 23, 2000
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| The Swiss 7TM Search Tool
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Search the list of known 7TM protein sequences, by using such keywords as NK1, ACETYLCHOLINE, etc...
Submitted Oct 22, 2000
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| TMHMM
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Prediction of transmembrane helices in proteins.
Submitted Oct 22, 2000
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| Translator
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Online translator tool to convert DNA sequences into protein from up to 6 reading phases.
Submitted Mar 10, 2003
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| Web Primer
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DNA and Purpose Entry.
Submitted Oct 18, 2000
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| WU-BLAST2
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WU-BLAST2 with post-processing of the output integrates multiple biological information resources into a graphical overview.
Submitted Oct 17, 2000
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