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Protocols

TBLASTX specifications

Information


Unique identifier OMICS_01000
Name TBLASTX
Alternative name Translated BLAST: tblastx
Interface Web user interface
Restrictions to use None
Input data An accession number or a sequence of interest.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Eric W Sayers

Publication for Translated BLAST: tblastx

TBLASTX citations

 (1473)
library_books

Analysis of Theileria orientalis draft genome sequences reveals potential species level divergence of the Ikeda, Chitose and Buffeli genotypes

2018
BMC Genomics
PMCID: 5921998
PMID: 29703152
DOI: 10.1186/s12864-018-4701-2

[…] Following annotation each independent gene track was assessed using Evidence Modeler v1.1.1 [] to generate the final annotation with the following weights applied (EST: coding2genome = 7, blastn = 2, tblastx = 2. Protein: protein2genome = 10, blastx = 2. Ab initio: augustus = 2, snap = 1, genemark = 1). Additionally, annotations were manually curated by visual inspection and comparison to those tr […]

library_books

Extensive mitochondrial gene rearrangements in Ctenophora: insights from benthic Platyctenida

2018
BMC Evol Biol
PMCID: 5924465
PMID: 29703131
DOI: 10.1186/s12862-018-1186-1

[…] ngle mt contig. In contrast, the mt genomes of the two Coeloplana species were initially each assembled on several contigs (8 for C. yulianicorum and 3 for C. loyai). Therefore, for these two species tBlastx searches were performed using the mt genome of Mnemiopsis leidyi as query [] with the aim of identifying additional mt contigs. The mt contigs thereby identified were then elongated by read ma […]

library_books

Elucidation of the anti hyperammonemic mechanism of Lactobacillus amylovorus JBD401 by comparative genomic analysis

2018
BMC Genomics
PMCID: 5918772
PMID: 29695242
DOI: 10.1186/s12864-018-4672-3

[…] alignment. The gene model was predicted by Glimmer [] and compared with the following public databases: COGs [], Interpro [], Pfam [], Prints [], PROSITE [], Smart [], Swissprot [], and Tigrfams []. Tblastx [] was used to reanalyze intergenic regions for ORFs. Hmmer [] on pfam 5.4 was used for motif analysis. Stringent parameters were used to identify tRNAs by trnascan-se [] and ribosomal binding […]

library_books

piRNA Profiling of Dengue Virus Type 2 Infected Asian Tiger Mosquito and Midgut Tissues

2018
Viruses
PMCID: 5923507
PMID: 29690553
DOI: 10.3390/v10040213

[…] A tBLASTx search of the Ae. albopictus genome and transcripts, using the Ae. aegyti PIWI protein family genes as queries, was performed. Significant gene expansion was observed in PIWI sub-family protei […]

library_books

Genome analysis of the freshwater planktonic Vulcanococcus limneticus sp. nov. reveals horizontal transfer of nitrogenase operon and alternative pathways of nitrogen utilization

2018
BMC Genomics
PMCID: 5902973
PMID: 29661139
DOI: 10.1186/s12864-018-4648-3

[…] The structure and similarity of the nitrogenase subunits for the different compared cyanobacteria, including the novel planktonic Vulcanococcus limneticus sp. nov., was assessed by tBLASTX [] with > 50% similarity hits and 50 bp of alignment lengths. […]

library_books

Genome wide analysis of the transition to pathogenic lifestyles in Magnaporthales fungi

2018
Sci Rep
PMCID: 5897359
PMID: 29651164
DOI: 10.1038/s41598-018-24301-6

[…] atabase for use with the second TEannot script. This latter stage is run twice in order to perform a complete genome-wide annotation using multiple classifiers. A step is also performed which employs tBLASTx and BLASTx from the BLAST + vr. 2.2.31 package to search Repbase vr. 20.05, a curated data bank of TEs. Both stages were run using default settings and also incorporated the Pfam vr. 27.0 data […]

Citations

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TBLASTX institution(s)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA

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