If the candidate protein sequence is a remote homolog, direct gene modeling from BLAST-like database searches may have different predictions compared to more sophisticated SSBGP tools. (A) EMBL DNA sequence HSCKBG was compared with the protein sequences in the nr sequence database usingBLASTX. Hits with Pvalue < 10−20 were discarded, the top remaining corresponded to a fragmentary protein sequence gi:553231. Not surprisingly, only a small fraction of the actual gene was recovered using this homolog by either GENEWISE orPROCRUSTES. Other choices of homologs may have yielded different predictions but none of them by themselves appears to be perfect. Conversely, the gene model derived directly from theBLASTX search reproduces the exonic structure of the gene fairly well. Thus, even though upon discarding the close homologs, the remaining proteins individually showed only little overall similarity to the encoded protein product, as a collection they enable to walk its exonic structure. (B) If database protein sequences with hits below P-value = 10−20 are discarded, BLASTX is able to detect significant similarity between only one of the encoded exons in EMBL sequence HSPAC3G and the remaining protein sequences in the database. But with the top homolog among these, the SSBGP tools (GENEWISE in particular) are able to infer the correct exonic structure, picking up both the additional upstream exons. This is because the SSBGP tools are able to detect more distant sequence relationships than BLASTX with our choice of thresholds or because (as in this case) coding exons occur in low-complexity regions, which are usually masked when performingBLASTX searches to avoid large numbers of false positives. (C) In another case, direct gene modeling from BLASTX searches and SSBGP tools can complement each other to produce more accurate gene predictions. As inA and B, HSP hits belowP-value = 10−20 were ignored after comparing EMBL sequence HSFOLA with the nonredundant protein sequence database.
