Motif, Domain, Profile, Pattern, & Repeat Searches

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

2nd Window 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.
[more info][14074]

2nd Window BCM Search Launcher: General Protein Sequence/Pattern Searches
[Baylor College of Medicine] A site with multiple tools to search a protein sequence for patterns.
[more info][12330]

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 Blocks WWW Server
[Fred Hutchinson Cancer Research Center] Tools for the detection and verification of protein sequence homology.
[more info][10440]

2nd Window CKAAP Database
[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.
[more info][13764]

2nd Window Construction of profiles for PROSITE
[ISREC] This is a guide on how to generateprofile entries for the PROSITE database.
[more info][12191]

2nd Window DEJAVU Server
[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.
[more info][12244]

2nd Window Distant Homologies
[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.
[more info][11985]

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 DOTLET
[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.
[more info][12208]

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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 for registered users.
[more info][13604]

2nd Window eMOTIF
[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.
[more info][10447]

2nd Window GeneOrder
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.
[more info][13591]

2nd Window InterPro
[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.
[more info][13762]

2nd Window MAR-Finder
[NCGR] MAR-Finder uses statistical inference to deduce the presence of matrix association regions. A user name and password is required, but registration is free.
[more info][10399]

2nd Window MEME
[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.
[more info][11261]

2nd Window 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.
[more info][11014]

2nd Window Motif Explorer
[CBC] A tool developed to search PIR or Arabidopsis database using a protein or DNA sequence.
[more info][10368]

2nd Window Motif Search Tool
[NCBI] (MoST) “MoST will scan the indicated database iteratively until convergence, by adding segments selected at each iteration to the original block.”
[more info][12204]

2nd Window MOTIF: Searching Protein and Nucleic Acid Sequence Motifs
[Genome Net] Finds protein motifs in query sequence and gives structural information on the found motifs.
[more info][11998]

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2nd Window 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.
[more info][13761]

2nd Window PatScan
[Argonne National Laboratory] A pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which is input.
[more info][10371]

2nd Window Pattern Search
[Pole Bio-Informatique Lyonnais] A form allowing submission of a sequence to perform a pattern search.
[more info][10409]

2nd Window PatternFind Server
[ISREC] Searches the PROSITE database with a Perl script.
[more info][10463]

2nd Window Pfam
[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.
[more info][12195]

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 PlantsP
[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.
[more info][13642]

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

2nd Window Pratt Pattern Discovery
[EBML] A tool that allows the user to search for patterns conserved in a set of protein sequences.
[more info][10468]

2nd Window 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.”
[more info][12198]

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2nd Window 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.”
[more info][12197]

2nd Window ProDom: The Protein Domain Database
[INRA] “The ProDom protein domain database consists of an automatic compilation of homologous domains.”
[more info][12199]

2nd Window ProfileScan Server
[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.
[more info][10469]

2nd Window ProSite Protein
[ExPASy] A searchable dictionary of proteins and patterns. Identifies to which family of proteins a sequence belongs.
[more info][12680]

2nd Window PrositeScan Server
[ISREC] Uses a Perl script to scan the Amos Bairochs ProSite database.