Multiple sequence alignment Benchmark Data set
1. 汇总: 序列比对标准数据集: http://www.drive5.com/bench/
This is a collection of multiple alignment benchmarks in a uniform
format that is convenient for further analysis. All files are in
FASTA format, with upper-case letters used to indicate aligned
columns.
See References below for original sources of benchmark data.
Benchmarks are:
--------------------------1---------------------------
bali2dna
BALIBASE v2, reverse-translated to DNA
bali2dnaf
Bali2dbn, with frame-shifts induced by random insertions of one
or two nucleotides into the middle 50% of exactly one sequence
in each set.
bali3
BALIBASE v3.
bali3pdb
BALIS, the structural subset of BALIBASE v3.
bali3pdbm
MU-BALIS, i.e. BALIS re-aligned by MUSTANG.
---------------------------2--------------------------
ox
OXBENCH.
oxm
MU-OXBENCH, i.e. OXBENCH re-aligned by MUSTANG.
oxx
OXBENCH-X, i.e. the Extended set in OBENCH.
---------------------------3--------------------------
prefab4
PREFAB v4.
prefab4ref
PREFAB-R, i.e. the pair-wise reference pairs in PREFAB v4.
prefab4refm
MU-PREFAB-R, i.e. PREFAB-R re-aligned by MUSTANG.
---------------------------4--------------------------
sabre
Consistent multiple alignments constructed from SABMARK v1.65.
sabrem
MU-SABRE, i.e. SABRE re-aligned by MUSTANG.
-----------------------------------------------------
Directory structure under each benchmark is:
in/
Input sequences.
ref/
Reference alignments. Upper-case regions indicate conservative
regions that are intended for use in assessment. Lower-case regions
should not be used.
info/
Contains ids.txt (list of set identifiers that are filenames in ref/
and in/), nrseqs.txt (number of sequences in each set), and
pctids.txt (%id in conservative regions in each set).
Download page for qscore :http://www.drive5.com/bench/bench.tar.gz
This is a quality scoring program that compares two multiple sequence alignments: an alignment to be evaluated (the "test" alignment) and a second alignment that is believed to be correct (the "reference" alignment). The program outputs the following scores:
- The PREFAB Q score (aka the Balibase SPS score or the Developer score).
- The Modeler score
- The Cline et al. shift score
- The Balibase TC (total column) score
Balibase标准数据库地址: http://www.lbgi.fr/balibase/
References
----------
Thompson JD, Koehl P, Ripp R, Poch O (2005) BAliBASE 3.0: latest
developments of the multiple sequence alignment benchmark. Proteins
61: 127-136.
Bahr A, Thompson JD, Thierry JC, Poch O (2001) BAliBASE (Benchmark
Alignment dataBASE): enhancements for repeats, transmembrane
sequences and circular permutations. Nucleic Acids Res 29: 323-326.
Thompson JD, Plewniak F, Poch O (1999) BAliBASE: a benchmark
alignment database for the evaluation of multiple alignment programs.
Bioinformatics 15: 87-88.
Van Walle I, Lasters I, Wyns L (2005) SABmark--a benchmark for
sequence alignment that covers the entire known fold space.
Bioinformatics 21: 1267-1268.
Raghava GP, Searle SM, Audley PC, Barber JD, Barton GJ (2003)
OXBench: a benchmark for evaluation of protein multiple sequence
alignment accuracy. BMC Bioinformatics 4: 47.
Edgar RC (2004) MUSCLE: multiple sequence alignment with high
accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
