title: TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB.
abstract: Transcriptome Auto-annotation Conducting Tool (TACT) is a newly developed web-based automated tool for conducting functional annotation of transcripts by the integration of sequence similarity searches and functional motif predictions. We developed the TACT system by integrating two kinds of similarity searches, FASTY and BLASTX, against protein sequence databases, UniProtKB (Swiss-Prot/TrEMBL) and RefSeq, and a unified motif prediction program, InterProScan, into the ORF-prediction pipeline originally designed for the 'H-Invitational' human transcriptome annotation project. This system successively applies these constituent programs to an mRNA sequence in order to predict the most plausible ORF and the function of the protein encoded. In this study, we applied the TACT system to 19 574 non-redundant human transcripts registered in H-InvDB and evaluated its predictive power by the degree of agreement with human-curated functional annotation in H-InvDB. As a result, the TACT system could assign functional description to 12 559 transcripts (64.2%), the remainder being hypothetical proteins. Furthermore, the overall agreement of functional annotation with H-InvDB, including those transcripts annotated as hypothetical proteins, was 83.9% (16 432/19 574). These results show that the TACT system is useful for functional annotation and that the prediction of ORFs and protein functions is highly accurate and close to the results of human curation. TACT is freely available at http://www.jbirc.aist.go.jp/tact/.
authors.affiliation: Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics Consortium, AIST Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan.
authors.forename: Chisato
authors.initials: C
authors.lastname: Yamasaki
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Kawashima
authors.forename: Fusano
authors.initials: F
authors.lastname: Todokoro
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Imamizu
authors.forename: Makoto
authors.initials: M
authors.lastname: Ogawa
authors.forename: Motohiko
authors.initials: M
authors.lastname: Tanino
authors.forename: Takeshi
authors.initials: T
authors.lastname: Itoh
authors.forename: Takashi
authors.initials: T
authors.lastname: Gojobori
authors.forename: Tadashi
authors.initials: T
authors.lastname: Imanishi
mesh_terms: D020816:Amino Acid Motifs; D019295:Computational Biology / Q000379:methods; D018076:DNA, Complementary / Q000737:chemistry; D030562:Databases, Protein; D020224:Expressed Sequence Tags / Q000737:chemistry; D006801:Humans; D020407:Internet; D016366:Open Reading Frames; D011506:Proteins / Q000235:genetics / Q000502:physiology; D012333:RNA, Messenger / Q000737:chemistry*; D017421:Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D012984:Software; D018511:Systems Integration; D014584:User-Computer Interface
chemical_list: D018076:DNA, Complementary; D011506:Proteins; D012333:RNA, Messenger