SPANNER: taxonomic assignment of sequences using pyramid matching of similarity profiles.

ABSTRACT:

Background

Homology-based taxonomic assignment is impeded by differences between the unassigned read and reference database, forcing a rank-specific classification to the closest (and possibly incorrect) reference lineage. This assignment may be correct only to a general rank (e.g. order) and incorrect below that rank (e.g. family and genus). Algorithms like LCA avoid this by varying the predicted taxonomic rank based on matches to a set of taxonomic references. LCA and related approaches can be conservative, especially if best matches are taxonomically widespread because of events such as lateral gene transfer (LGT).

Results

Our extension to LCA called SPANNER (similarity profile annotater) uses the set of best homology matches (the LCA Profile) for a given sequence and com

SUBMITTER: Porter MS 

PROVIDER: S-EPMC3712219 | biostudies-literature | 2013 Aug

REPOSITORIES: biostudies-literature