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AliWABA -- alignment on the web through an A-Bruijn approach
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| Conduct multiple alignment of protein sequences with Repeated and Shuffled Elements.
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BCM Search Launcher
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| Determine protein function for a DNA sequence or find genomic sequence corresponding to a gene.
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BLAST 2 SEQUENCES
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| Compare two nucleotide or protein sequences using a local alignment algorithm. |
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BLAST Filter and GraphAlign -- Rule-based Formation and Analysis of Multiple DNA and Protein Sequences
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| Build and analyze sets of related DNA and protein sequences. |
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BLAST2SRS -- a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases
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| Retrieve user-defined subsets of homologous protein sequences.
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BLASTO: a tool for searching orthologous groups
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| Search for orthologous groups
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BLAT Search Genome
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| Quickly find sequences of 95% and greater similarity of length 40 bases or more for DNA or 80% and greater similarity of length 20 amino acids or more for protein in a genome. |
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BiasViz -- visualization of amino acid biased regions in protein alignments
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| A tool to graphically study local amino acid composition in protein sequences of a multiple sequence alignment.
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COMPASS server for remote homology inference
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| Construct local alignments and detect homology based on the comparison of multiple sequence alignments
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CRASP -- Analysis of Coordinated Substitutions in Multiple Alignments of Protein Sequences
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| Detect and analyze coordinated substitutions in multiple alignments of protein sequences.
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Cascade PSI-BLAST web server -- a remote homology search tool for relating protein domains
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| Identify distant homologous protein sequences.
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Clustal W
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| Perform multiple DNA or protein sequences alignments.
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ConSurf-DB -- evolutionary conservation profiles of protein structures database
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| Automatically calculate evolutionary conservation scores of key amino acid residues and map them on protein structures.
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Consensus -- An Alignment Server for Reliable Comparative Modeling with Distant Templates
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| Find concensus regions among distantly related protein sequences.
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DIALIGN -- Multiple DNA and Protein Sequence Alignment at BiBiServ
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| Align multiple DNA or protein sequences.
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DNA and Protein Sequence Manipulation Suite 2
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| Conduct a variety of analysis of DNA and protein sequences. |
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Do-It-Yourself Sequence Comparison using WU-Blast 2.0
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| Use this blast tool to blast query sequence against your own collection of sequences.
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EMBOSS Pair wise Alignment
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| Compare two sequences with either local or global alignment algorithms. |
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EXProt -- A database for proteins with an experimentally verified function
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| Search for protein sequences for which the function has been experimentally verified.
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Expresso -- automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee
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| Perform high-quality multiple protein sequence alignments.
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FFAS03 -- a server for profile–profile sequence alignments
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| Conduct protein alignment analysis, multiple sequence alignment, and comparative modeling.
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GeneTrees -- a phylogenomics resource for prokaryotes
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| Search for pre-computed alignments and phylogenetic trees for all protein sequences from 325 fully sequenced and annotated prokaryote genomes.
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HHrep -- de novo protein repeat detection and the origin of TIM barrels
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| Detect repeated sequences in a protein sequence using HMM-HMM comparison.
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Kalign, Kalignvu and Mumsa -- web servers for multiple sequence alignment
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| Conduct multiple alignments and subsequent quality evaluation. |
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LALIGN -- local alignment tool
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| Compare two protein or DNA sequences for local similarity and show the local sequence alignments.
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M-Coffee -- a meta-method for computing multiple sequence alignments by combining alternative alignment methods
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| Web server that computes multiple sequence alignments (MSAs) by running several MSA methods and combining their output into one single model.
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MAVL/StickWRLD -- analyzing structural constraints using interpositional dependencies in biomolecular sequence alignments
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| Detect and display both positive and negative inter-positional correlations in nucleic acid and protein sequences. |
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MAVL/StickWRLD for protein -- visualizing protein sequence families to detect non-consensus features
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| Visualize and survey the model-training sequences to discover and characterize possible dependencies among protein sequences.
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MIPS -- analysis and annotation of genome information
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| Search for protein sequence-related information based on whole-genome analysis.
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MPsrch --True Smith and Waterman algorithm search tool
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| Find similar sequences to a query protein sequence from SWISS-PROT using an exhaustive true Smith and Waterman algorithm.
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Meta-BASIC -- Detecting distant protein homology
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| Detect distant similarity between proteins based on consensus alignments of meta profiles. |
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Multlin -- Multiple sequence alignment tool
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| Perform multiple sequence alignment with hierarchical clustering.
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NCBI BLAST Portal Site
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| Find similar sequences to a query sequence from various sequence databases.
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NCBI Protein database
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| Search for comprehensive information on protein.
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ORFeus -- detection of distant homology using sequence profiles and predicted secondary structure
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| Perform automated and sensitive protein sequence similarity search.
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One-Block CYRCA -- an automated procedure for identifying multiple-block alignments from single block queries
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| Identify multiple-block alignments from single block queries of protein sequence.
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OntoBlast function -- from sequence similarities directly to potential functional annotations by ontology terms
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| Find information about potential functions of proteins.
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PA-GOSUB -- a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization
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| Search for sequences, predicted GO molecular functions and predicted subcellular localizations of more than 107,000 proteins from 10 model organisms.
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PAL2NAL -- robust conversion of protein sequence alignments into the corresponding codon alignments
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| Convert a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment.
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PARALIGN -- rapid and sensitive sequence similarity searches powered by parallel computing technology
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| Identify distantly related sequences in both nucleotide and amino acid sequence databases. |
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PISCES -- recent improvements to a PDB sequence culling server
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| Produce lists of sequences from the Protein Data Bank (PDB) using a number of entry- and chain-specific criteria and mutual sequence identity.
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PRALINE -- a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information
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| Perform multiple protein sequence alignment and integrate information from database homology searches to generate a homology-extended multiple alignment.
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PROMALS web server for accurate multiple protein sequence alignments
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| Construct multiple protein sequence alignment
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PVS -- Protein Variability Server
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| A web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery.
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PepBank -- a database of peptides based on sequence text mining and public peptide data sources
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| A searchable archive for peptide sequences and associated biological data.
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Peptide sequence and literature database
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| Search for information on peptide sequence and literature.
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PipeAlign -- a new toolkit for protein family analysis
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| Use this protein family analysis tool to search for sequence homologues in protein and 3D structure databases, the definition of the hierarchical relationships within and between subfamilies. |
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PrediSi -- Prediction of Signal Peptides and their Cleavage Positions
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| Predict signal peptide sequences and their cleavage positions in bacterial and eukaryotic amino acid sequences. |
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Predict Protein
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| Perform sequence analysis and structure prediction for an amino acid sequence |
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ProBias -- a web-server for the identification of user-specified types of compositionally biased segments in protein sequences
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| A web-server that searches a protein sequence for CBS composed of user-specified amino acid types.
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QuasiMotiFinder -- protein annotation by searching for evolutionarily conserved motif-like patterns
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| Search for evolutionarily conserved motif-like patterns in protein sequences. |
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RANKPROP -- Protein Ranking by Network Propagation
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| A web server for protein remote homology detection.
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RE-MuSiC: A Tool for Multiple Sequence Alignment with Regular Expression Constraints
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| Construct a multiple sequence alignment by incorporating biological knowledge of sequences (such as motifs, patterns, signatures or fingerprints) into the alignment procedure.
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REPPER —- repeats and their periodicities in fibrous proteins
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| Detect and analyze regions with short gapless repeats in protein sequences or alignments.
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Radar -- Rapid Automatic Detection and Alignment of Repeats in protein sequences
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| Find sequence repeats in a protein sequence.
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Randseq --Random protein sequence generator
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| Generate a random protein sequence.
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RefSeq -- Reference Sequence database
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| Find sequences representing genomes, transcripts, and proteins. |
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Refseq -- a curated non-redundant sequence database of genomes, transcripts and proteins
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| Retrieve curated, non-redundant reference mRNA sequences from NCBI. |
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Reverse Translate Tool
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| Translate a protein (amino acid) sequence to its corresponding nucleotide sequence.
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SCANMOT -- searching for similar sequences using a simultaneous scan of multiple sequence motifs
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| Search for similarities between proteins by simultaneous matching of multiple motifs.
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SCANPS -- a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser
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| Protein sequence database searching.
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SIRW -- a web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches
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| Search protein/nucleotide databases with keywords and a sequence motif. |
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SledgeHMMER -- A web server for batch searching the Pfam database
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| Carry out batch searching of Pfam database using the 'hmmpfam' program. |
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Standard protein-protein BLAST [blastp]
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| Find similar sequences to a query sequence from protein databases
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Swiss EMBnet node web server
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| Use a collection of bioinformatics tools at this portal site. |
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SwissProt
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| Retrieve comprehensive protein information
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TCDB -- Transporter Classification Database for membrane transport protein analyses and information
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| Search for comprehensive information on documented and predicted membrane transport protein.
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Tcoffee@igs -- A web server for computing, evaluating and combining multiple sequence alignments
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| Conduct and evaluate multiple sequence alignments for protein, DNA and RNA.
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The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis
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| Conduct various analysis to protein sequences use a suite of software tools.
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The MPI Bioinformatics Toolkit for protein sequence analysis
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| Conduct protein sequence and structure analysis using a suite of software tools.
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The PSSH database of alignments between protein sequences and tertiary structures
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| Investigate the tertiary structure of a protein of interest. |
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The PredictProtein server
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| Predict protein structure and function based on protein sequence.
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UniParc -- UniProt archive, a repository of all protein sequences
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| Search a comprehensive repository of all protein sequences.
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UniProt -- the Universal Protein Resource
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| A central resource on protein sequences and functional annotation.
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UniRef -- Clustered sets of related sequences from UniProt
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| Search or download the Clustered sets of related sequences from UniProt.
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UniqueProt -- creating representative protein sequence sets
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| Create representative, unbiased data sets of protein sequences.
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WAViS -- Tools for Handling, Visualization and Presentation of Multiple DNA/protein sequence Alignments
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| Prepare publication-quality pictures of DNA or protein multiple sequence alignments. |
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WU-Blast2 -- Basic Local Alignment Search Tool
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| Find regions of nucleotide or protein sequence similarity quickly, with minimum loss of sensitivity.
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Wise2 -- Intelligent algorithms for DNA searches
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| Compare a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.
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YOGY -- a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms
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| Retrieve protein orthologs and associated Gene Ontology terms from nine eukaryotic model organisms.
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eProbalign: generation and manipulation of multiple sequence alignments using partition function posterior probabilities
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| Compute multiple sequence alignments from partition function posterior probabilities.
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enoLOGOS -- a versatile web tool for energy normalized sequence logos
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| Generate sequence logos from DNA and protein sequences.
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trome, trEST and trGEN -- Databases of Predicted Protein Sequences
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| Search and analyze hypothetical protein sequences. |
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xREI -- a phylo-grammar visualization webserver
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| Explore a range of pre-defined phylo-grammars.
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