| Name |
Description |
| BLOCKS |
HMM-like profile HMM library; ungapped |
| CDD |
Conserved domain database (PFAM plus SMART) |
| Interpro |
A unified resource combining PROSITE, PRINTS, ProDom and Pfam, SMART,
and TIGRfam |
| iProClass database |
From the Protein Information Resource |
| MetaFAM |
Proteins compiled from six databases |
| PFAM |
Profile HMM library |
| PIR-ALN |
Database of alignments |
| PRINTS |
Protein fingerprints from SWISS-PROT/TrEMBL |
| ProDom |
Uses PSI-BLAST to cluster Swiss-Prot |
| Prosite |
A dictionary of protein motifs |
| SMART |
Simple Modular Architecture Research Tool |
| TIGRFAMs |
HMM library of protein families |
| Program |
Description |
| AMAS
(Analyse Multiply Aligned Sequences) |
At the European Bioinformatics Institute; used to analyze pre-made MSAs |
| CINEMA |
Colour INteractive Editor for Multiple Alignments |
| ClustalW |
At the European Bioinformatics Institute and other sites |
| ClustalX |
Download by FTP |
| DIALIGN |
Especially useful for local MSA. From the University of Bielefeld, Germany |
| Match-Box
Web Server 1.3 |
From the University of Namur, Belgium |
| MultAlin |
From INRA (http://www.inra.fr/), Toulouse |
| Multiple Sequence alignment
Version 2.0 |
At the GeneStream server of the Institut de Génétique Humaine (http://www2.igh.cnrs.fr/home.eng.html) |
| Multiple Sequence
Alignment version 2.1 |
From Washington University, St. Louis |
| Musca |
From the IBM Bioinformatics Group |
| PileUp |
Available through the SeqWeb or UNIX versions of GCG |
| T-COFFEE |
Slower but more accurate than ClustalW for distantly related proteins |