Figure 4
Validation of spruce FLcDNAs by comparison of ORF lengths (A) and cDNA lengths (B) of 297 spruce FLcDNAs with matching gymnosperm FLcDNAs in the public domain. The 6,464 FLcDNAs were compared to a collection of 872 gymnosperm sequences from SwissProt using BLASTX ([71]; release 50.1 of June 13th, 2006) annotated as full-length (excluding predicted proteins derived from genomic DNA). This comparison identified 297 homologous pairs. A spruce-gymnosperm FLcDNA pair was considered homologous if (1) the best gymnosperm protein BLASTX match exceeded a stringent threshold (% identity ≥ 50%; score value > 95) and (2) the reciprocal TBLASTN analysis identified the same spruce FLcDNA with a score value equal to or within 10% of the best match. ORF and cDNA lengths for gymnosperm sequences were extracted from the SwissProt records, and spruce ORF lengths were predicted using the EMBOSS getorf program. Strong correlations were observed for both ORF and cDNA lengths between spruce and gymnosperm sequences for the available test set of 297 homologous pairs.