CASA: a server for the critical assessment of protein sequence alignment accuracy.
CONCLUSIONS
A public server for evaluating the accuracy of protein sequence alignment methods is presented. CASA is an implementation of the alignment accuracy benchmark presented by Sauder et al. (Proteins, 40, 6-22, 2000). The benchmark currently contains 39321 pairwise protein structure alignments produced with the CE program from SCOP domain definitions. The server produces graphical and tabular comparisons of the accuracy of a user's input sequence alignments with other commonly used programs, such as BLAST, PSI-BLAST, Clustal W, and SAM-T99.


BACKGROUND
The server is located at http://capb.dbi.udel.edu/casa.
Kahsay
Robel Y
RY
Delaware Biotechnology Institute and Department of Electrical and Computer Engineering, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA.
Wang
Guoli
G
Dongre
Nataraj
N
Gao
Guang
G
Dunbrack
Roland L
RL
D000465:Algorithms; D002138:Calibration; D003205:Computing Methodologies; D030562:Databases, Protein; D005069:Evaluation Studies as Topic; D020407:Internet; D009317:National Library of Medicine (U.S.); D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods* / Q000592:standards*; D020539:Sequence Analysis, Protein / Q000379:methods; D012984:Software; D014481:United States
D011506:Proteins