Table 2.
Sequence alignment programs, family HMM profiles and motifs databases.*
| Method | Description/URL |
|---|---|
| BLAST or PSI-BLAST (149) | Database searching http://www.ncbi.nlm.nih.gov/BLAST/ |
| ClustalW (150) | Multiple sequence alignment http://www.ebi.ac.uk/clustalw/ |
| GPCRHMM (42) | Identification and classification of GPCRs http://gpcrhmm.cgb.ki.se |
| HMAP (57) | Profile-to-profile alignment including secondary and tertiary structure information. http://trantor.bioc.columbia.edu/hmap/ |
| Hydropathy profile alignment | Direct alignment of hydropathy profiles for database search http://bioinformatics.weizmann.ac.il/hydroph/hydroph.html |
| Hydropathy pattern matching | Conversion of representative profile into pattern of peaks/troughs for database search |
| PHAT search (35) | http://blocks.fhcrc.org/sift/PHAT_submission.html |
| PSI-BLAST with compositional bias (149) | Database searching allowing for differences in composition in membrane proteins. http://www.ncbi.nlm.nih.gov/blast/ |
| PFAM (50) | Database of protein families including HMMs and sequence alignments http://www.sanger.ac.uk/Software/Pfam/ |
| PRED-GPCR (43) | Identification and classification of GPCRs http://bioinformatics.biol.uoa.gr/PRED-GPCR |
| PRINTS (15) | Database of protein family fingerprints (motifs) http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/ |
| PROSITE (14) | Database of protein families including patterns and profiles http://www.expasy.ch/prosite/ |
| T-Coffee (56) | Advanced multiple sequence alignment http://www.igs.cnrs-mrs.fr/Tcoffee/tcoffee_cgi/index.cgi |
| TM-PSI (44) | Matching of predicted TM regions from TMHMM within PSI-BLAST profiles for database search |
*
Code for other methods mentioned in the text is usually available from the authors