Identifying coding exons by similarity search: Alu-derived and other potentially misleading protein sequences

The search for significant local similarities with known protein sequences is a powerful method for interpreting anonymous cDNA sequences or locating coding exons within genomic DNA sequences at a stage where the average contig size is still very small. The BLASTx program, implemented on the National Center for Biotechnology Information server, allows a sensitive search of all putative translations of a nucleotide query sequence against all...