MaxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences.

ABSTRACT:

Motivation

The task of reconstructing a genomic sequence from a particular species is gaining more and more importance in the light of the rapid development of high-throughput sequencing technologies and their limitations. Applications include not only compensation for missing data in unsequenced genomic regions and the design of oligonucleotide primers for target genes in species with lacking sequence information but also the preparation of customized queries for homology searches.

Results

We introduce the maxAlike algorithm, which reconstructs a genomic sequence for a specific taxon based on sequence homologs in other species. The input is a multiple sequence alignment and a phylogenetic tree that also contains the target species. For this target species, the algorithm com

SUBMITTER: Menzel P 

PROVIDER: S-EPMC3031029 | biostudies-literature | 2011 Feb

REPOSITORIES: biostudies-literature