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Table 2 Feature comparison web-based transcript analysis platforms

From: TRAPID: an efficient online tool for the functional and comparative analysis of de novoRNA-Seq transcriptomes

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
  1. aBasic web-start version.