TransPS statistics

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Citations per year

Number of citations per year for the bioinformatics software tool TransPS
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Tool usage distribution map

This map represents all the scientific publications referring to TransPS per scientific context
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Associated diseases

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TransPS specifications

Information


Unique identifier OMICS_11469
Name TransPS
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Input to TransPS includes the set of preassembled contigs and the BLASTX search results containing the alignment of the contigs to the set of reference amino acid sequences.
Output data The output of TransPS includes contigs in three different groups, accepted contigs (A), scaffolded contigs (S), and unused/redundant contigs (R). The contigs in R could be the real redundancy due to genetic variants or different transcripts due to alternative splicing. In order to provide users with detailed account of how the assembly of a particular config is done, a matching map between the original contigs and the corresponding reference protein sequences used in the scaffolding algorithm is also provided.
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 1.1.0
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Mingming Liu

Publication for TransPS

TransPS citation

library_books

Comparative performance of transcriptome assembly methods for non model organisms

2016
BMC Genomics
PMCID: 4964045
PMID: 27464550
DOI: 10.1186/s12864-016-2923-8

[…] mal transcriptome assembly strategy, comparing four assembly methods: a) de novo assembly using Trinity [, ], b) reference-based re-assembly using proteomic and genomic resources from Ae. aegypti, c) TransPS [] using the Ae. aegypti proteome and d) genome-guided assembly by Cufflinks [] using the recently sequenced Ae. albopictus genome and the well-annotated Ae. aegypti genome. The quality of the […]


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TransPS institution(s)
Department of Computer Science, Virginia Tech, Blacksburg, VA, USA; Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA
TransPS funding source(s)
This work was supported by National Institutes of Health via grant AI085091.

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