BioTech FYI Center

Protein Function Assignment

Protein Function Assignment
Search Pattern, motif, Profiles domains, families
  • ScanProsite (Search a protein sequence against PROSITE pattern database at ExPASy, CH)
  • PPSearch (Search a protein sequence against PROSITE pattern database with graphical output at EBI, UK)
  • FingerPRINTScan (Search a protein sequence against protein motif fingerprints database PRINTS )
  • Scansite (Prediction of protein signaling sequence motifs at HIM, Boston, USA)
  • SearchPfam at Wustl or EBI (Search a protein against Pfam domain/family database)
  • CD-Search (Search a protein against CDD domain database, including Pfam and SMART, with RPS-BLAST at NCBI, USA)
  • eMOTIF Search (Assign putative function to new proteins by sequence comparison with IDENTIFY motif database at Stanford University, USA)
  • PROCAT (Search a protein structure agains the PROCAT database of 3D enzyme active site templates)
  • Meta-MEME (motive buiding at San Diego Supercomputer Centre, SDSC, Ca, USA)
  • eMOTIF Maker (Generate motifs that describe protein families or superfamilies ats Stanford University, USA)
  • Modules (mobile protein domains database)
  • HSSP (Database of homology-derived structures and sequences of proteins at EBI)
  • eMATRIX Search (Function prediction by sequence analysis using minimal-risk scoring matrices at Stanford University, USA)
  • PROSCAN (Search a protein sequence against PROSITE pattern database allowing mismatches at PBIL, Lyon, Fr)
  • PFSCAN (Search protein against different profile databases at ISREC; also searches PROSITE and Pfam patterns)
  • BLOCKS Search (Search a protein against BLOCKS database; also searches PRINTS)
  • DART (Domain Architecture Retrieval Tool at NCBI, USA)
  • InterProScan or InterPro Search (Search a protein against the integrated protein domains and functional sites database InterPro at EBI, UK)
  • COGnitor (Search a protein agains the COG database at NCBI)
  • iProCass Search (Search a protein against PIR's integrated protein class database at Georgetown University, USA)
  • SMART (Simple Modular Architecture Research Tool at EMBL; also searches Pfam)
  • MEME (Multiple EM for Motive Elicitation: Motive discovery at San Diego Supercomputer Centre, SDSC, Ca, USA)
  • ProDom (Protein domain database at Toulouse, Fr)
  • DOMO (homologous protein domain families database)
  • SBASE (Protein domain library at ICGEB, It)
  • 3Motif (Find protein (domain)s with defined 3D motifs at Stanford University, USA (runs only with Netscape and Chime plugin))
  • GeneQuiz (Automated analysis of protein sequences at EMBL)
Search, computation & analysis of pathways
  • KEGG (Search and computation tools at KEGG pathway database, Kyoto, Jp)
  • aMAZE (Query tools for pathway analysis at EBI, UK)
Protein-Protein interactions
Protein Annotation
  • PAA (Protein Annotator's Assistant at EBI, UK)
  • Artemis (Free (large-) DNA sequence viewer and annotation tool at the Sanger Center, UK)
Automatic alert for related new sequence
  • Sequence Alerting System (E-mail alert for daily searched new homologues of query sequence at EMBL, Heidelberg)
  • Swiss-Shop (Automatically receive alerts upon new submissions of related protein sequences)
  • PubCrawler (Automated alerting service that scans daily updates to PubMed and GenBank databases at Trinity College Dublin, Ireland)
  • Microbial Genomes Notification (Receive notifications by e-mail about new complete genomes in GenBank)
RNA Analysis Tools
  • RNA World (Links to RNA resources from IMB Jena Biocomputing Group, Jena, Germ.)
Protein Function Assignment