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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]

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BMC Plant Biology

ISSN: 1471-2229

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