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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.