IsoInfer specifications

Information


Unique identifier OMICS_01319
Name IsoInfer
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages C, C++
Computer skills Advanced
Version 0.9.1
Stability Stable
Source code URL http://www.cs.ucr.edu/~jianxing/IsoInfer0.9.1.html
Maintained Yes

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Documentation


Maintainer


  • person_outline Jianxing Feng <>

Publication for IsoInfer

IsoInfer in publications

 (2)
PMCID: 4331715
PMID: 25708199
DOI: 10.1186/1471-2164-16-S2-S15

[…] transcriptome assembly usually begins by mapping rna-seq reads to the reference genome. after that, different algorithms can be used to infer transcripts from mapped reads, including cufflinks [,], isoinfer [], isolasso [], slide [], cliiq [], mitie [], etc. this ab initio approach is different from the de novo approach where reference genome is not used (such as abyss [], trinity [], etc.), […]

PMCID: 3227660
PMID: 22140575
DOI: 10.1371/journal.pone.0028318

[…] parameters (allowed two mismatches). then we used those mapping information to infer the isoforms transcribed from brain and cell lines base on the human gene annotation information of ucsc by isoinfer ., next, we calculated the protein-coding capacities of all brain and cell line transcripts using cpc which incorporates the sequence features into a support vector machine to assess […]


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IsoInfer institution(s)
School of Life Sciences and Technology, Tongji University, China; Department of Computer Science, University of California, Riverside, CA, USA; Tsinghua University, Beijing, China
IsoInfer funding source(s)
Supported in part by a CSC scholarship, NSF grant IIS-0711129, and NIH grants 2R01LM008991 and AI078885.

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