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

Francesco MusacchiaRemo Sanges


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. Annocript is distributed under the GNU General Public License (version 3 or later) and is freely available at


Dec 11, 1999·Nucleic Acids Research·A Bairoch
Oct 9, 2002·Genome Research·Jason E StajichEwan Birney
Aug 13, 2003·Bioinformatics·Ian Korf
Jun 18, 2005·BMC Bioinformatics·Liisa B KoskiGertraud Burger
Apr 11, 2008·BMC Bioinformatics·Ralf Schmid, Mark L Blaxter
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Nov 22, 2011·Nucleic Acids Research·Anne MorgatAlain Viari
Nov 20, 2012·Nucleic Acids Research·UNKNOWN UniProt Consortium
Dec 1, 2012·Nucleic Acids Research·Aron Marchler-BauerStephen H Bryant

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