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TransGeneScan specifications

Information


Unique identifier OMICS_09917
Name TransGeneScan
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Perl
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Haixu Tang

Publication for TransGeneScan

TransGeneScan citations

 (4)
library_books

Targeted metatranscriptomics of compost derived consortia reveals a GH11 exerting an unusual exo 1,4 β xylanase activity

2017
Biotechnol Biofuels
PMCID: 5667448
PMID: 29118851
DOI: 10.1186/s13068-017-0944-4

[…] which were identified using Silva [] and Rfam [] reference databases with an e-value cutoff of 1 × 10−5. Non-ribosomal RNA reads were de novo assembled with Trinity [] and genes were predicted using TransGeneScan []. Expression levels were calculated with eXpress [] and Bowtie2 []. The phylogenetic origin of predicted ORFs was analyzed using MEGAN v6 [] and the Lowest Common Ancestor algorithm at […]

call_split

Effects of silver nanoparticles on nitrification and associated nitrous oxide production in aquatic environments

2017
Sci Adv
PMCID: 5540255
PMID: 28782034
DOI: 10.1126/sciadv.1603229
call_split See protocol

[…] sortmerna/). The trinity de novo assembly pipeline was used to assemble the high-quality paired-end mRNA reads (, ). Resulting sequences were filtered to remove contigs of less than 300 bp in length. TransGeneScan (http://sourceforge.net/projects/transgenescan/) was used to predict open reading frames. Transcripts were assigned to taxonomic affiliations by binning to the best hit (BLASTP, e value […]

library_books

A Meta Transcriptomics Survey Reveals Changes in the Microbiota of the Chinese Mitten Crab Eriocheir sinensis Infected with Hepatopancreatic Necrosis Disease

2017
Front Microbiol
PMCID: 5405120
PMID: 28491058
DOI: 10.3389/fmicb.2017.00732

[…] vo assembled with Trinity software (http://trinityrnaseq.github.io/; version trinityrnaseq-r2013-02-25) using default parameters as previously described (Grabherr et al., ). ORFs were predicted using TransGeneScan software (http://sourceforge.net/projects/transgenescan/). Non-redundant gene catalogs were constructed with an identity of 95% and a coverage of 90% using CD-HIT software (http://www.bi […]

library_books

Selective Dicer Suppression in the Kidney Alters GSK3β/β Catenin Pathways Promoting a Glomerulocystic Disease

2015
PLoS One
PMCID: 4370407
PMID: 25799508
DOI: 10.1371/journal.pone.0119142

[…] moting its proteasomal degradation, while phosphorylation in S9 of GSK3β mediates β-catenin stabilization [].Since GSK3β mRNA has multiple target sites for several members of the miRNA200 family (www.transgenescan.com) the suppression of miRNA200 family in Dicer cKO mice [] could determine GSK3β cytosolic accumulation and therefore β-catenin inhibition. Upregulation of Pdk-1 is an additional mecha […]

Citations

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TransGeneScan institution(s)
School of Informatics and Computing, Indiana University, Bloomington, IN, USA

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