QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction.

ABSTRACT:

Motivation

Secondary structure prediction accuracy (SSPA) in the QuanTest benchmark can be used to measure accuracy of a multiple sequence alignment. SSPA correlates well with the sum-of-pairs score, if the results are averaged over many alignments but not on an alignment-by-alignment basis. This is due to a sub-optimal selection of reference and non-reference sequences in QuanTest.

Results

We develop an improved strategy for selecting reference and non-reference sequences for a new benchmark, QuanTest2. In QuanTest2, SSPA and SP correlate better on an alignment-by-alignment basis than in QuanTest. Guide-trees for QuanTest2 are more balanced with respect to reference sequences than in QuanTest. QuanTest2 scores correlate well with other well-established benchmarks.

Availa

SUBMITTER: Sievers F 

PROVIDER: S-EPMC9881607 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature