Program Names | Website | Reference |
---|---|---|
Gene Prediction | ||
Glimmer | [15] | |
FragGeneScan | [18] | |
Prodigal | [17] | |
GeneMark | [16] | |
Sequence Comparison | Â | Â |
BLAST | [22] | |
HMMER | [27] | |
Multiple Alignment | ||
Muscle | [29] | |
Kalign | [32] | |
Distance Matrix | ||
Phylip | [33] | |
Clustering | ||
Markov chain Clustering (MCL) | [28] | |
Sequence manipulation | ||
EMOSS | [20] | |
Functional Annotation | ||
InterProScan | [40] | |
Annotation Database | ||
UniprotKB / SwissProt | [19] | |
Pfam | [41] | |
Gene3D | [42] | |
SMART | [43] | |
ProDOM | [44] | |
FingerPRINTScan | [45] | |
PANTHER | [46] | |
HAMAP | [47] | |
PIR | [48] | |
TIGRFAM | [49] | |
InterPro | [50] | |
MetaCyc | [51] | |
KEGG | [52] | |
SignalP | [53] | |
TMHMM | [54] | |
Phobius | [55] | |
GeneOntology | [56] | |
SQL Database | ||
SQLite | Â |