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TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB
Transcriptome Auto-annotation Conducting Tool (TACT) is a web-based automated prediction tool of functional annotation of the transcripts by integrating two kinds of similarity searches, BLASTX[1] and FASTY[2], against protein sequence databases and a unified motif prediction program, InterProScan[3], into the ORF-prediction pipeline. TACT is originally developed as an automatic functional annotation pipeline for an international cooperative project entitled "Human Full-length cDNA Annotation Invitational" (abbreviated as H-Invitational or H-Inv) project[4, 5] but may be applied to predict function of transcriptome of any species.
TACT is provided by at URL; http://h-invitational.jp/tact/index.html
>> Input sequence data to TACT
>> TACT submit views
>> TACT annotation view
>> Reference

>Input sequence data to TACT

TACT web-based interfaces consist of three main views, TACT top, TACT submit view and TACT annotation view.
Upload nucleotide sequence data to TACT in one of the three formats;
1) copy & paste nucleotide sequences(s) in FASTA.
2) upload a single or multi- FASTA or DDBJ format flat file(s) from local disk.
3) enter DNA databank accession number(s).
Click on "Submit" to submit the sequence data to TACT annotation system.

Fig. 1 TACT top
[NOTES]
  • The maximum sequence length analyzed by TACT is 30,000 bp
  • Submit within 10 nucleotide sequences.
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>TACT submit views

Confirm your query data and type your email address for TACT to send you the URL for annotation results in TACT submit view. Please select the analysis and enter your e-mail address to receive TACT annotation. Click on "Submit annotation" to start analysis. e.g. AB002356

If you wish to cancel and go back to the top page, click on "Cancel".

Fig.2-1 TACT submit view
The notice of starting the calculation will appear. Please confirm the URLs for TACT annotation results. Click on URL to browse TACT annotation results. A message of "Now analyzing" will be shown while the analysis is on the way.

Please keep the URLs to browse TACT annotation results.

Fig.2-2 TACT submit view
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>TACT annotation view

The TACT annotation view shows all the annotation of the input sequence. It consists of six sections, Auto-functional annotation information section, Mapping information section, cDNA information section, Predicted ORF section, Predicted motif information section and Predicted subcellular localization section.

The annotation results will be shown for the query in each section of TACT annotation view.

Auto-annotation information section
a) Corresponding H-Invitational transcript (HIT) ID
b) Definition of the protein of the sequence
c) Similarity category of the gene (original standard H-InvDB)
Category I: Identical to known human protein.
Category II: Similar to known protein.
Category III: InterPro domain-containing protein.
Category IV: Conserved hypothetical protein.
Category V: Hypothetical protein.


Fig 3-1 Classification of similarity categories
d) ORF prediction and translation
e) Data source: evidence for definition of the protein
f) species, % identity and % coverage to the evidence.
g) Similarity search tool or InterProScan evidence (FASTY, BlastX, InterProScan) of the definition.
h) Codon adaptation index (CAI)

Fig 3-2 TACT annotation view: auto-functional annotation section
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Mapping information section
a) Corresponding H-Invitational cluster (HIX) ID
b) Chromosome number
c) Location in the chromosome
d) Chromosomal band
e) Strand of the Genome

cDNA information section
a) DNA databank accession number
b) Definition of DNA databank
c) Species
d) Length of cDNA
e) Clone No., tissue-type, cell-type and developmental stage of sequence origin
f) EC number
g) Gene name
h) Nucleotide sequence


Fig 3-3 TACT annotation view: mapping and cDNA information section
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Predicted ORF section
a) Predicted ORF
b) Translation
c) Frame
d) Amino acid length

Fig 3-4 TACT annotation view: predicted ORF section
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Predicted motif information section
a) Size and location of the predicted motif in predicted ORF
b) InterPro ID, name, type
c) GO ID, term, description

Fig 3-5 TACT annotation view: predicted motif section
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>References

  1. Altschul, S.F., et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res, 1997. 30(17): p. 3389-3402.
  2. Pearson, W.R., et al., Comparison of DNA sequences with protein sequences. Genomics, 1997. 46(1): p. 24-36.
  3. Mulder, N.J., et al., InterPro, progress and status in 2005. Nucleic Acids Res, 2005. 33(Database issue): p. D201-5.
  4. Imanishi, T., et al., Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol, 2004. 2(6): p. 856-75.
  5. Yamasaki, C., et al., Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational database (H-InvDB). Gene, 2005. 364: p. 99-107.
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