Table 2 Feature comparison web-based transcript analysis platforms
Features | Blast2GOa | KAAS | TRAPID |
|---|---|---|---|
Sequence similarity search | NCBI BLAST | BLAST (bi-directional) | RAPSearch2 |
ORF finding | No | No | Yes |
Frameshift correction | No | No | FrameDP |
Reference database | NCBI non redundant database | Curated KEGG genes | OrthoMCL-DB version 5, PLAZA 2.5 |
Functional annotation | Gene Ontology, InterProScan, Enzyme codes, KEGG | KEGG (KEGG Orthology groups) | Gene Ontology, Protein domains (InterPro/PFAM) |
Enrichment analysis | Yes | No | Yes |
Protein alignments | No | No | MUSCLE |
Phylogenetic trees | No | No | FastTree, PhyML |
Others | advanced stand-alone graphical user interface | graphical pathway maps | ORF length meta-annotation, share experiments with other users |