Canonical, stable, general mapping using context schemes.

ABSTRACT:

Motivation

Sequence mapping is the cornerstone of modern genomics. However, most existing sequence mapping algorithms are insufficiently general.

Results

We introduce context schemes: a method that allows the unambiguous recognition of a reference base in a query sequence by testing the query for substrings from an algorithmically defined set. Context schemes only map when there is a unique best mapping, and define this criterion uniformly for all reference bases. Mappings under context schemes can also be made stable, so that extension of the query string (e.g. by increasing read length) will not alter the mapping of previously mapped positions. Context schemes are general in several senses. They natively support the detection of arbitrary complex, novel rearrangements rela

SUBMITTER: Novak AM 

PROVIDER: S-EPMC4757953 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature