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Old 02-23-2015, 03:09 AM   #4
frankM
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Location: Italy

Join Date: Feb 2015
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You may want to use Annocript. It was just published on Bioinformatics and permits annotation of any type of transcriptome (both nucleotides and peptides). It is a pipeline that runs BLAST programs and gives the best HIT against SwissProt and TrEMBL or UniRef, CDD domains, rFam. Moreover it also presents which transcripts could be putative lncRNAs. It gives a lot of outputs: a complete table with the annotation, plots and statistics, blast output in GFF3 format, fasta file with the putative coding and long non coding sequences.

The program is straightforward to use and open source. Freely downloadable at:

github.com/frankMusacchia/Annocript

There you will also find some plugins to make differential expression analyses starting from a table with raw counts and the output of Annocript.
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