Frameshift alignment: statistics and post-genomic applications.

ABSTRACT:

Motivation

The alignment of DNA sequences to proteins, allowing for frameshifts, is a classic method in sequence analysis. It can help identify pseudogenes (which accumulate mutations), analyze raw DNA and RNA sequence data (which may have frameshift sequencing errors), investigate ribosomal frameshifts, etc. Often, however, only ad hoc approximations or simulations are available to provide the statistical significance of a frameshift alignment score.

Results

We describe a method to estimate statistical significance of frameshift alignments, similar to classic BLAST statistics. (BLAST presently does not permit its alignments to include frameshifts.) We also illustrate the continuing usefulness of frameshift alignment with two 'post-genomic' applications: (i) when finding pse

SUBMITTER: Sheetlin SL 

PROVIDER: S-EPMC4253828 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature