Table 1.
List of bioinformatics tools available in CFGP 2.0
| Category | Name | Input data | References |
|---|---|---|---|
| Sequence search | BLAST | Sequences | (12) |
| BLAST2 | Sequences | (12) | |
| BLASTMatrix | Sequences | (11) | |
| ID of functional domains | InterPro Scan | Sequences | (13) |
| Phylogenetic analysis | ClustalW | Sequences | (14) |
| DNAML | Alignment | (15) | |
| PROML | Alignment | (15) | |
| DNAPARS | Alignment | (15) | |
| PROTPARS | Alignment | (15) | |
| PHYML | Alignment | (16) | |
| ID of secreted proteins | SignalP 3.0 | Sequences | (17) |
| SigCleave | Sequences | (18) | |
| SigPred | Sequences | (19) | |
| RPSP | Sequences | (20) | |
| SecretomeP | Sequences | (21) | |
| Subcellular localization | PSortII | Sequences | (22) |
| predictNLS | Sequences | (23) | |
| ChloroP | Sequences | (24) | |
| TargetP | Sequences | (25) | |
| Prediction of trans-membrane helices | TMHMM2 | Sequences | (26) |
| Prediction of RNA secondary structure | tRNAScan-SE | Sequences | (27) |
| mFold 3.2 | Sequences | (28) | |
| Post-translational modification | NetCGlyc | Sequences | (29) |
| NetNGlyc | Sequences | – | |
| NetOGlyc | Sequences | (30) | |
| NetPhos | Sequences | (31) | |
| Conserved motif search | MEME | Sequences | (32) |
A total of 27 tools in nine categories are available via the Favorite browser of CFGP 2.0.