Table 1.
Software used for isoform feature prediction
| Feature Group | Software | Reference |
|---|---|---|
| Amino acid composition | EMBOSS-6.6.0 | [39] |
| Sequence features | EMBOSS-6.6.0 | [39] |
| Gravy | GRAVY calculator | (no warranty) |
| Transmembrane segments | MEMSAT 3.0 | [40] |
| Secondary structure | PSIPRED 4.0 | [41] |
| Intrinsically disordered regions | DISOPRED 3.16 | [42] |
| Signal peptides | SinglP 4.0 | [43] |
| Subcellular localization | YLoc | [44] |
| PEST regions | EMBOSS-6.6.0 | [39] |
| Low complexity regions | EMBOSS-6.6.0 | [39] |
| Coiled coils | EMBOSS-6.6.0 | [39] |
| Phosphorylation sites | NetPhos-3.1 | [45] |
| N-linked glycosylation sites | NetNGlyc-1.0c | [45] |
| O-GalNAc-glycosylation sites | NetOglyc-3.1d | [45] |
| Domains (Pfam) | InterProScan 5.24 | [29] |
| Motifs (Prosite) | InterProScan 5.24 | [29] |