Design and assessment of a fast algorithm for identifying specific probes for human and mouse genes

Abstract

Motivation: Mammalian genomes are highly complex. To identify the unique sequences of each gene in a mammalian gene database containing tens of thousands of DNA sequences is a computation intensive task. With the advent of parallel genetic analysis methods such as microarrays and the availability of more and more whole genome sequences of organisms, an algorithm allowing speedy identification of the unique gene probes for functional studies of individual genes will be a very useful tool.

Results: We have developed a fast algorithm as well as a software program based on the algorithm for identifying gene specific probes of complex organisms. The algorithm was applied to the assemblies of gene sequences and was highly efficient for large databases such as the TIGR human THC and mouse TC databases. The results were assessed with the BLAST sequence alignment software. Two probe data sets have been compiled to contain specific probes for around 100 000 putative human gene transcripts and 70 000 putative mouse gene transcripts.

Availability: The gene specific probes for the putative human and mouse genes referenced in the TIGR gene indices are available at: ftp://genestamp.ibms.sinica.edu.tw/pub/SpecificP/. The software program and the source codes are available upon request.