Annocript: a flexible pipeline for the annotation of transcriptomes able to identify putative long noncoding RNAs | Zendy

Francesco Musacchia | Zendy; Swaraj Basu | Zendy; Giuseppe Petrosino | Zendy; Marco Salvemini | Zendy; Remo Sanges | Zendy

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Annocript: a flexible pipeline for the annotation of transcriptomes able to identify putative long noncoding RNAs

Author(s) -

Francesco Musacchia,

Swaraj Basu,

Giuseppe Petrosino,

Marco Salvemini,

Remo Sanges

Publication year - 2015

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btv106

Subject(s) - transcriptome , annotation , pipeline (software) , computer science , mit license , coding (social sciences) , software , computational biology , license , long non coding rna , source code , rna , biology , gene , genetics , artificial intelligence , gene expression , operating system , statistics , mathematics

The eukaryotic transcriptome is composed of thousands of coding and long non-coding RNAs (lncRNAs). However, we lack a software platform to identify both RNA classes in a given transcriptome. Here we introduce Annocript, a pipeline that combines the annotation of protein coding transcripts with the prediction of putative lncRNAs in whole transcriptomes. It downloads and indexes the needed databases, runs the analysis and produces human readable and standard outputs together with summary statistics of the whole analysis.

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