PlantTA statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

PlantTA specifications

Information


Unique identifier OMICS_21437
Name PlantTA
Alternative name TIGR Plant Transcript Assemblies database
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained No

Maintainer


This tool is not available anymore.

Publication for TIGR Plant Transcript Assemblies database

PlantTA citations

 (16)
call_split

Involvement of Potato (Solanum tuberosum L.) MKK6 in Response to Potato virus Y

2014
PLoS One
PMCID: 4128675
PMID: 25111695
DOI: 10.1371/journal.pone.0104553
call_split See protocol

[…] otato Oligo Chip Initiative: http://pgrc-35.ipk-gatersleben.de/pls/htmldb_pgrc/f?p=194∶1); The Gene Index Project (http://compbio.dfci.harvard.edu/tgi/); and TIGR Plant Transcripts Assemblies (http://plantta.jcvi.org/search.shtml).To identify StMKK6 orthologues we searched the UniProt database using the BLASTp algorithm . Multiple-sequence alignments were performed using the MAFFT programme (versi […]

library_books

Deep sequencing transcriptome analysis of low temperature perception in a desert tree, Populus euphratica

2014
BMC Genomics
PMCID: 4035058
PMID: 24884892
DOI: 10.1186/1471-2164-15-326

[…] net/poplar). All unigenes were also compared with data in publicly available databases including 13,991 unassembled P. euphratica ESTs from GenBank and assembled ESTs from other poplar species in the TIGR Plant Transcript Assemblies database. […]

library_books

Epigenetic patterns newly established after interspecific hybridization in natural populations of Solanum

2013
Ecol Evol
PMCID: 3810873
PMID: 24198938
DOI: 10.1002/ece3.758

[…] oEdit 7.0.9 (Hall ).Analysis of DNA similarity was carried out using the BLASTn packages implemented at The Institute for Genomic Research (TIGR; http://www.jcvi.org/; http://blast.jcvi.org/euk-blast/plantta_blast.cgi). […]

library_books

Pearl millet [Pennisetum glaucum (L.) R. Br.] consensus linkage map constructed using four RIL mapping populations and newly developed EST SSRs

2013
BMC Genomics
PMCID: 3606598
PMID: 23497368
DOI: 10.1186/1471-2164-14-159

[…] The resulting ESTs were cleaned of rRNA, vector, ligator and poor quality sequences using SeqClean (http://compbio.dfci.harvard.edu/tgi/software/) and assembled using the Plant Transcript Assemblies (PLANTTA) pipeline [], using the TGICL assembler [] with the following parameters: retention requiring a 50 bp minimum match, 95% minimum identity in the overlap region and 20 bp maximum unmatched over […]

call_split

Transcriptomic Profiling during the Post Harvest of Heat Treated Dixiland Prunus persica Fruits: Common and Distinct Response to Heat and Cold

2012
PLoS One
PMCID: 3516522
PMID: 23236430
DOI: 10.1371/journal.pone.0051052
call_split See protocol

[…] ih.gov/pubmed/); (2) the Prunus persica EST collection at ESTreeDB database (http://www.itb.cnr.it/estree) ; (3) the TIGR transcript assembly database for all public Prunus persica and plant ESTs, or PlantTA (http://plantta.tigr.org) and (4) The Arabidopsis Information Resource (http://www.arabidopsis.org). Sequences longer than 100 nucleotides were annotated as highly similar to the first BLAST […]

call_split

Genetic and physiological analysis of Rht8 in bread wheat: an alternative source of semi dwarfism with a reduced sensitivity to brassinosteroids

2012
J Exp Bot
PMCID: 3421992
PMID: 22791821
DOI: 10.1093/jxb/ers138
call_split See protocol

[…] tachyon unspliced gene sequences (release 1.0, www.modelcrop.org; ftp://ftp.ensemblgenomes.org/pub/plants/release-3/fasta/brachypodium_distachyon/cdna/). Wheat assembled ESTs were downloaded from the TIGR Plant Transcript Assemblies database (ftp://ftp.tigr.org/pub/data/plantta/Triticum_aestivum/). For all data sets, a local BLAST database was produced using the command formatdb. A local similarit […]

Citations

Looking to check out a full list of citations?

PlantTA institution(s)
The Institute for Genomic Research, Rockville, MD, USA
PlantTA funding source(s)
Supported in part by grants from the National Science Foundation Plant Genome Research Program (DBI-0218166, DBI-0321538, DBI-0321663, DBI-313887, DBI-0321460) and from the U.S. Department of Agriculture (USDA 59-1275-5-364).

PlantTA reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review PlantTA