Efficient computation of absent words in genomic sequences.

ABSTRACT:

Background

Analysis of sequence composition is a routine task in genome research. Organisms are characterized by their base composition, dinucleotide relative abundance, codon usage, and so on. Unique subsequences are markers of special interest in genome comparison, expression profiling, and genetic engineering. Relative to a random sequence of the same length, unique subsequences are overrepresented in real genomes. Shortest words absent from a genome have been addressed in two recent studies.

Results

We describe a new algorithm and software for the computation of absent words. It is more efficient than previous algorithms and easier to use. It directly computes unwords without the need to specify a length estimate. Moreover, it avoids the space requirements of index struc

SUBMITTER: Herold J 

PROVIDER: S-EPMC2375138 | biostudies-literature | 2008 Mar

REPOSITORIES: biostudies-literature