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 known proteins in a matter of seconds. From an analysis of the current databases, I report a set of protein sequences exhibiting high local similarity to Alu repeat or vector sequences. These entries can lead to misleading interpretations of similarity searches. During the course of this study, the protease of a human spumaretrovirus was found to have integrated the 3' end half of the U2 snRNA.