Table 1 Software used for isoform feature prediction
From: CuAS: a database of annotated transcripts generated by alternative splicing in cucumbers
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] |