Summary: 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. Availability and implementation: Annocript is distributed under the GNU General Public License (version 3 or later) and is freely available at https://github.com/frankMusacchia/Annocript.

Annocript: A flexible pipeline for the annotation of transcriptomes able to identify putative long noncoding RNAs / Musacchia, Francesco; Basu, Swaraj; Petrosino, Giuseppe; Salvemini, Marco; Sanges, Remo. - In: BIOINFORMATICS. - ISSN 1367-4803. - 31:13(2015), pp. 2199-2201. [10.1093/bioinformatics/btv106]

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

Sanges, Remo
Project Administration
2015

Abstract

Summary: 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. Availability and implementation: Annocript is distributed under the GNU General Public License (version 3 or later) and is freely available at https://github.com/frankMusacchia/Annocript.
31
13
2199
2201
10.1093/bioinformatics/btv106
http://bioinformatics.oxfordjournals.org/
Musacchia, Francesco; Basu, Swaraj; Petrosino, Giuseppe; Salvemini, Marco; Sanges, Remo
File in questo prodotto:
File Dimensione Formato  
Musacchia et al. - 2015 - Annocript a flexible pipeline for the annotation .pdf

non disponibili

Descrizione: Copyright: The Authors. Free Access on Review Website.
Tipologia: Versione Editoriale (PDF)
Licenza: Non specificato
Dimensione 85.53 kB
Formato Adobe PDF
85.53 kB Adobe PDF   Visualizza/Apri   Richiedi una copia

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/20.500.11767/68492
Citazioni
  • ???jsp.display-item.citation.pmc??? 41
  • Scopus 74
  • ???jsp.display-item.citation.isi??? 67
social impact