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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)
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- 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)
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Search, computation & analysis of pathways |
- KEGG (Search and computation tools at KEGG pathway database, Kyoto, Jp)
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- aMAZE (Query tools for pathway analysis at EBI, UK)
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Protein-Protein interactions |
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- PAA (Protein Annotator's Assistant at EBI, UK)
- Artemis (Free (large-) DNA sequence viewer and annotation tool at the Sanger Center, UK)
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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)
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- 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)
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- RNA World (Links to RNA resources from IMB Jena Biocomputing Group, Jena, Germ.)
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