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Table 1 Comparison of existing software tools designed to work on whole transcriptome datasets

From: afterParty: turning raw transcriptomes into permanent resources

Name

In active development

Sequence data type

Interface

Annotations

PartiGene [17]

No

Sanger EST reads

Command-line

BLAST, InterProScan, KEGG, prot4est

Cbrowse [18]

No

Assembed contigs + read mapping data

Web

None

BRIGEP [20]

No

Assembled transcripts

Web

BLAST, InterProScan

TranscriptomeBrowser [21]

Yes

Public microarray data

Java GUI

Existing ontologies

afterParty

Yes

Roche 454 raw reads or assembled contigs

Web

BLAST, InterProScan

  1. The scope of this table is restricted to tools designed for transcriptome analysis - genome browsers are not included. We define a project as being in active development if the most recent change to the source code repository was made less than one year ago.