Protein Motif Recognition

Current biosequence analysis programs must be able to recognize protein-level homology or pattern in DNA sequences containing spurious insertions and deletions (indels) of nucleotides. We present a method for nding simple protein motifs in such sequences, building upon the standard dynamic programming sequence alignment algorithm. The commonly used frameshift penalty is replaced by a probabilistic model of the indel rate, providing both a means of controlling selectivity and a guide for evaluation. Furthermore, given a threshold on edit distance, the algorithm avoids computation of cells of the dynamic programming matrix that could not possibly be part of an acceptable alignment path. The method is practical for scanning large DNA sequence databases for protein motifs