Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding-3

52 sequences [56]) and a collection of 1,409 previously published poplar sequences from the non-redundant (NR) division of GenBank ([57], the NR release of December 19, 2006) annotated as full-length (excluding predicted proteins derived from genomic DNA). FLcDNAs were excluded from the analysis when the in-house BLAST-aided ORF detection software identified a FLcDNA as problematic according to the following categories: truncation at the 5'-end (319), truncation at the 3'-end (50), frameshift (12), stop codon in the middle of an ORF (9), or inverted insert (3) [see Additional file ]. No problematic features were identified in the remaining 4,271 FLcDNAs. This comparison identified 2,774 homologous Arabidopsis-poplar pairs and 288 homologous poplar transcript pairs. A FLcDNA pair was considered homologous if (1) the top BLASTX match exceeded a stringent threshold (% identity ≥ 50%; expect value ≤ 1e) and (2) the reciprocal TBLASTN analysis identified the same poplar FLcDNA with a score value equal to or within 10% of the top match. ORF lengths for Arabidopsis and public poplar sequences were extracted from the TAIR and NR records, respectively, and poplar ORF lengths from this study were predicted using either the EMBOSS getorf or in-house BLAST-aided programs (see Figure 2 legend). The greyscale shading of each hexagon represents poplar FLcDNA abundance. ORF lengths for three Arabidopsis-poplar pairs and eight homologous poplar transcript pairs differed by more than 500 aa and are not included in the figure.<p><b>Copyright information:</b></p><p>Taken from "Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding"</p><p>http://www.biomedcentral.com/1471-2164/9/57</p><p>BMC Genomics 2008;9():57-57.</p><p>Published online 29 Jan 2008</p><p>PMCID:PMC2270264.</p><p>