Table 3.
Bioinformatics tools integrated into the PAM
| Method | Description | Reference |
|---|---|---|
| Methods to determine sequence intrinsic properties | ||
| pI | Isoelectric point and molecular mass | |
| SEG | Detection of low-complexity regions | (27) |
| COIL | Detection of coiled-coil structures | (29) |
| SIGSEQ | Detection of signal peptides | (30) |
| MEMSAT | Transmembrane segment prediction | (28) |
| Homology search methods | ||
| RPS-BLAST | Reverse position specific BLAST | |
| PSI-BLAST | Sequenced-based homology search | (11) |
| FROST | Fold recognition method for detecting remote homologues | (14) |
| Miscellaneous methods | ||
| PSORTb | Prediction of subcellular localization | (17) |
| Jalview | Multiple sequence alignment editor | (35) |
| InterProScan | Integrated protein motif detection, including the following software: | (31) |
| Motif and functional signature detection methods | ||
| ProfileScan | Find motifs using profiles | (57) |
| ScanRegExp | Find motifs using regular expressions | (58) |
| FPrintScan | Find multiple motifs | (59) |
| Domain detection using HMM methods | ||
| HMMSmart | Genetically mobile domains from SMART | (8) |
| HMMPfam | Protein family domains from PFAM | (12) |
| HMMTigr | Protein families from TIGR institute | (32) |
| HMMPIR | Protein families from PIR | (60) |
| HMMPanther | Protein families subdivided into functionally related subfamilies | (61) |
| SuperFamily | Proteins of known 3D structure | (62) |
| Gene3D | Protein families in complete genomes | (63) |
| Method to split protein sequences into domains | ||
| BlastProDom | Defines domains in protein sequences | (64) |
| Methods to find sequence intrinsic properties | ||
| SignalPHMM | Prediction of signal peptide | (65) |
| TMHMM | Prediction of transmembrane helices in proteins | (66) |