title: CASA: a server for the critical assessment of protein sequence alignment accuracy.
abstract: 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.
authors.affiliation: Delaware Biotechnology Institute and Department of Electrical and Computer Engineering, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA.
authors.forename: Robel Y
authors.initials: RY
authors.lastname: Kahsay
authors.forename: Guoli
authors.initials: G
authors.lastname: Wang
authors.forename: Nataraj
authors.initials: N
authors.lastname: Dongre
authors.forename: Guang
authors.initials: G
authors.lastname: Gao
authors.forename: Roland L
authors.initials: RL
authors.lastname: Dunbrack
mesh_terms: 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
chemical_list: D011506:Proteins