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Table 1 The comparison between algal functional annotation tool (AFAT) [[22]] and AlgaePath

From: AlgaePath: comprehensive analysis of metabolic pathways using transcript abundance data from next-generation sequencing in green algae

Content

AFAT

AlgaePath

Species

Chlamydomonas reinhardtii

Chlamydomonas reinhardtii

Chlorella NC64A

Neodesmus sp. UTEX 2219-4

Search interface

Identifiers ID and keyword

Gene symbol, Gene ID from various database, keyword, DNA/protein sequences

Pathways information of each transcript

Yes, only pathway map (out link to KEGG)

Yes, combine pathway map with transcript abundance profiles under various conditions

Gene group analysis (Pathway enrichment)

Yes, only mark genes in a pathway map (out link to KEGG)

Yes, not only mark genes in a pathway map but with transcript abundance profiles under various conditions

Differentially expression genes

No

Yes, easily identify differentially expressed genes between two samples

Expression similar search

Yes, only provide identifier ID in the expression map

Yes, provide detail information of co-expression genes

Pathway map with gene expression profiles

No

Yes