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-7

D program. The getorf program identifies the longest stretch of uninterrupted sequence between a start (ATG) and stop codon (TGA, TAG, TAA) in the 5' to 3' direction for the predicted ORF. The BLAST-aided program detects ORFs by finding the starting methionine and stop codon in a poplar FLcDNA sequence relative to the same features in the most closely related Arabidopsis protein identified by BLASTX (E values < 1e). For this study, ORFs identified by the BLAST-aided method were utilized except in cases where the FLcDNA sequence did not show high similarity to an Arabidopsis protein, in which case the ORF identified by the getorf program was chosen. The presence and coordinates of the 5' second strand primer adaptor sequence (SSPA) and polyA tail were also noted. The regions between the 5'SSPA and the predicted ORF start and between the predicted ORF stop and the polyA tail were taken to be the 5' and 3' UTRs, respectively. The 5' SSPA and 3' polyA tail lengths were not included when determining UTR length.<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>