Motif, Domain, Profile, Pattern, & Repeat Searches
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Bioinformatics & Genomics
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Motif, Domain, Profile, Pattern, & Repeat Searches
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3 Dee – Database of Protein Domain Definitions
[European Bioinformatics Institute] 3Dee contains structural domain definitions for all protein chains in the Protein Databank (PDB) [EBI-MSD/RCSB] that have 20 or more residues and are not theoretical models.
BCM Search Launcher: General Protein Sequence/Pattern Searches
[Baylor College of Medicine] A site with multiple tools to search a protein sequence for patterns.
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.
[San Diego Supercomputer Center] The Conserved Key Amino Acid Positions database provides access to an analysis of structurally similar proteins with dissimilar sequences where key residues within a common fold are identified. CKAAP database provides CKAAPs of the representative set of proteins derived from the Combinatorial Extension algorithm and FSSP databases.
[Uppsala Software Factory] The input to the server is a pdb file with a secondary structure motif.The secondary structure elements (SSEs) of the pdb file will be assigned first (or given explicitly in a file).You may input superpositioning criteria based on which the server will find similiar secondary structure motifs.
[The International Center for Genetic Engineering and Biotechnology] This is an introductory tutorial for biologists interested in weak protein sequence similarities which can not be found with simple database search.
[ISREC] This is a java applet that does Dot Plots (pairwise sequence comparisons). This site also contains examples with interpretations of Dot Plots, including protein repeat regions and intron and exon patterns in DNA.
[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.
[Stanford Univ.] Ranks the motifs that it finds by both their specificity (expected false postives) and the number of supplied sequences that it covers (true positives). The twenty highest-scoring motifs are returned. This site also contains several other tools for sequence alignment and similarity searching, protein function identification and genome analysis.
Compare the numerical order of protein-coding genes in two genomes, using GenBank genome files. Or compare a user-created list of protein sequences with a genome or another list. Program creates a dotplot of matches in proteins coded by genes, plotted in numerical order along the genome (or list). Points are plotted at different levels of significance for matching amino acid sequences. Program also generates a clickable list of matches. Genome size limited to less than 250 kb.
[European Bioinformatics Institute] InterPro is an integrated documentation resource for protein families, domains andsites, developed initially as a means of rationalising the complementary efforts of thePROSITE, PRINTS, Pfam and ProDom database projects. Each combined InterProentry includes functional descriptions and literature references, and links are madeback to the relevant member database(s), allowing users to see at a glance whethera particular family or domain has associated patterns, profiles, fingerprints, etc.
[San Diego Supercomputing Center] Discovers motifs (highly conserved regions) in groups of related DNA or protein sequences using MEME and searches sequence databases using motifs using MAST.
Molecular Sequence Megaclassification
[Washington Univ., St. Louis] Provides access to a non-redundant molecular sequence collection that can be accessed by domain type of sequence.
MOTIF: Searching Protein and Nucleic Acid Sequence Motifs
[Genome Net] Finds protein motifs in query sequence and gives structural information on the found motifs.
PANAL Protein Analysis
[University of Minnesota] PANAL is an integrated resource for protein sequence analysis. The tool allows the user to simultaneously search a protein sequence for motifs from several databases, and to view the results as an intutive graphical summary.
[Washington University, St. Louis] Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains based on the Swissprot 38 and SP-TrEMBL 11 protein sequence databases.
[consortium of several research laboratories] This genomics site is oriented to plant functional genomics. The site maintains servers for analyzing protein sequence, searching for patterns, and plotting motifs. The site also discusses plant protein phosphorylation.
PRINTS BLAST Search
[University of Manchester] “This is an interface to a BLAST search of all protein sequences contained within the PRINTS database. The user entered sequence may be a protein or DNA sequence.”
PRINTS: Protein Fingerprint Database
[University of Manchester] “PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs usedto characterise a protein family; its diagnostic power is refined by iterative scanning of aSWISS-PROT/TrEMBL composite.”
[ISREC] Searches a single sequence against currently available profile databases. Also available is Frame-ProfileScan Server, which uses the new frame search option of the pfscan program to search a single DNA sequence against currently available protein profile databases.
[ISREC] Uses a Perl script to scan the Amos Bairochs ProSite database.