An enhanced RNA alignment benchmark for sequence alignment programs.

ABSTRACT:

Background

The performance of alignment programs is traditionally tested on sets of protein sequences, of which a reference alignment is known. Conclusions drawn from such protein benchmarks do not necessarily hold for the RNA alignment problem, as was demonstrated in the first RNA alignment benchmark published so far. For example, the twilight zone - the similarity range where alignment quality drops drastically - starts at 60 % for RNAs in comparison to 20 % for proteins. In this study we enhance the previous benchmark.

Results

The RNA sequence sets in the benchmark database are taken from an increased number of RNA families to avoid unintended impact by using only a few families. The size of sets varies from 2 to 15 sequences to assess the influence of the number of seque

SUBMITTER: Wilm A 

PROVIDER: S-EPMC1635699 | biostudies-literature | 2006 Oct

REPOSITORIES: biostudies-literature