title: Sequence search algorithm assessment and testing toolkit (SAT).
abstract: BACKGROUND
  The Sequence Search Algorithm Assessment and Testing Toolkit (SAT) aims to be a complete package for the comparison of different protein homology search algorithms. The structural classification of proteins can provide us with a clear criterion for judgment in homology detection. There have been several assessments based on structural sequences with classifications but a good deal of similar work is now being repeated with locally developed procedures and programs. The SAT will provide developers with a complete package which will save time and produce more comparable performance assessments for search algorithms. The package is complete in the sense that it provides a non-redundant large sequence resource database, a well-characterized query database of proteins domains, all the parsers and some previous results from PSI-BLAST and a hidden markov model algorithm.
  
  
  RESULTS
  An analysis on two different data sets was carried out using the SAT package. It compared the performance of a full protein sequence database (RSDB100) with a non-redundant representative sequence database derived from it (RSDB50). The performance measurement indicated that the full database is sub-optimal for a homology search. This result justifies the use of much smaller and faster RSDB50 than RSDB100 for the SAT.
  
  
  BACKGROUND
  A web site is up. The whole packa ge is accessible via www and ftp. ftp://ftp.ebi.ac.uk/pub/contrib/jong/SAT http://cyrah.ebi.ac.uk:1111/Proj/Bio/SAT http://www.mrc-lmb.cam.ac.uk/genomes/SAT In the package, some previous assessment results produced by the package can also be found for reference.
  
  
  BACKGROUND
  jong@ebi.ac.uk
authors.affiliation: European Bioinformatics Institute, EMBL Outstation, Cambridge, UK. jong@ebi.ac.uk
authors.forename: J
authors.initials: J
authors.lastname: Park
authors.forename: L
authors.initials: L
authors.lastname: Holm
authors.forename: C
authors.initials: C
authors.lastname: Chothia
mesh_terms: D000465:Algorithms; D016208:Databases, Factual; D011506:Proteins / Q000032:analysis*
chemical_list: D011506:Proteins