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Nucleic Acids Research Advance Access published online on November 6, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl785
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© 2006 The Author(s).
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

The TIGR Plant Transcript Assemblies database

Kevin L. Childs, John P. Hamilton, Wei Zhu, Eugene Ly, Foo Cheung, Hank Wu, Pablo D. Rabinowicz, Chris D. Town, C. Robin Buell and Agnes P. Chan*

The Institute for Genomic Research 9712 Medical Center Drive, Rockville, MD 20850, USA

*To whom correspondence should be addressed: Tel: +1 301 795 7862; Fax: +1 301 838 0208; Email: achan{at}tigr.org

Received August 15, 2006. Revised September 21, 2006. Accepted September 29, 2006.

The TIGR Plant Transcript Assemblies (TA) database (http://plantta.tigr.org) uses expressed sequences collected from the NCBI GenBank Nucleotide database for the construction of transcript assemblies. The sequences collected include expressed sequence tags (ESTs) and full-length and partial cDNAs, but exclude computationally predicted gene sequences. The TA database includes all plant species for which more than 1000 EST or cDNA sequences are publicly available. The EST and cDNA sequences are first clustered based on an all-versus-all pairwise sequence comparison, followed by the generation of consensus sequences (TAs) from individual clusters. The clustering and assembly procedures use the TGICL tool, Megablast and the CAP3 assembler. The UniProt Reference Clusters (UniRef100) protein database is used as the reference database for the functional annotation of the assemblies. The transcription orientation of each TA is determined based on the orientation of the alignment with the best protein hit. The TA sequences and annotation are available via web interfaces and FTP downloads. Assemblies can be retrieved by a text-based keyword search or a sequence-based BLAST search. The current version of the TA database is Release 2 (July 17, 2006) and includes a total of 215 plant species.


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