New annotation of the Lolium perenne genome described by Bryne et al, (2015)

<p>Annotation of the Lolium perenne genome described by Bryne <em>et al,</em>&nbsp;(2015, DOI: 10.1111/tpj.13037).</p> <p>To identify genic regions RNA sequencing data were aligned to the genome using Tophat (Tophat version: V2.0.11; Bowtie2 version: 2.1.0). Isoforms, of genes, were identified using Cufflinks (Version: 2.2.0). Open reading frames (ORF), were found using using program ORFpredictor (version: 3.0). Frame selection was assisted by BLASTX searching the proteomes of <em>Arabidopsis thaliana</em> (TAIR, version: 10), <em>Oryza sativa</em> (Ensembl)<em>, Gycine max </em>(Ensembl)<em>, Populus trichocarpa </em>(Ensembl)<em> and Manihot esculenta </em>(cassava, v4.1). The predicted CDS was back translated to annotate the GFF file created by Cufflinks for CDS using scripts kindly provided by Palmieri<em> et al.,</em> 2012 (doi: 10.1371/journal.pone.0046415). These results are included in the file LG_V2_full.gtf.</p> <p>Functional annoatation was using three sources. First, protein sequences were search against the <em>A. thaliana</em> proteome using BLASTP. Second, the proteins were search against the Swiss-Prot non-redundant protein database (<a href="http://www.uniprot.org/downloads">http://www.uniprot.org/downloads</a> downloaded 14/03/2016, UniProt Consortium, 2014), again using BLASTP. In the third step, the protein sequences were scanned against InterPro&#39;s signatures using InterProScan (Version: 5.16-55). These data are included in the file ALLXLOC.txt.</p>