A functional motif discovery algorithm for invertebrate EST sequence data

Abstract

We have developed a new algorithm for invertebrate expressed sequence tag (EST) analysis, termed as the fmEST algorithm, which consists of a systematic homology search, functional motif scanning, and clustering alignment. This study was undertaken to evaluate the validity of our fmEST algorithm in functional motif discovery for invertebrate EST sequence data. Out of 200 unidentified invertebrate ESTs, including 100 arthropod ESTs and 100 mollusk ESTs, 18 arthropod ESTs and 21 mollusk ESTs were identified as fmESTs that contained functional motifs. The nucleotide lengths of arthropod fmEST and mollusk fmEST sequences were distributed from 388 to 954 bp and from 222 to 742 bp, respectively. This result allowed us to annotate these invertebrate fmESTs as various functional genes, while they showed no significant homology to the gene information recorded in the international DNA databases using the conventional BLAST homology search program. In addition, another 1 arthropod EST and 23 mollusk ESTs were assembled into contigs with any identified fmESTs by clustering alignment. Based on these findings, we have concluded that our fmEST algorithm, involving the functional motif discovery procedure, is a valuable approach, enabling us to break new ground in undeveloped invertebrate EST analysis.