Name
Title | ||
|---|---|---|
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. Availability and implementation QuanTest2 is available at http://bioinf.ucd.ie/quantest2.tar, comprises of reference and non-reference sequence sets and a scoring script. Supplementary information Supplementary data are available at Bioinformatics online |
Year | DOI | Venue |
|---|---|---|
2020 | 10.1093/bioinformatics/btz552 | BIOINFORMATICS |
Field | DocType | Volume |
Data mining,Computer science,Protein secondary structure,Benchmarking | Journal | 36 |
Issue | ISSN | Citations |
1 | 1367-4803 | 0 |
PageRank | References | Authors |
0.34 | 0 | 2 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Fabian Sievers | 1 | 78 | 5.49 |
| Desmond G. Higgins | 2 | 1263 | 383.91 |