title: The effectiveness of position- and composition-specific gap costs for protein similarity searches.
abstract: BACKGROUND
  The flexibility in gap cost enjoyed by hidden Markov models (HMMs) is expected to afford them better retrieval accuracy than position-specific scoring matrices (PSSMs). We attempt to quantify the effect of more general gap parameters by separately examining the influence of position- and composition-specific gap scores, as well as by comparing the retrieval accuracy of the PSSMs constructed using an iterative procedure to that of the HMMs provided by Pfam and SUPERFAMILY, curated ensembles of multiple alignments.
  
  
  RESULTS
  We found that position-specific gap penalties have an advantage over uniform gap costs. We did not explore optimizing distinct uniform gap costs for each query. For Pfam, PSSMs iteratively constructed from seeds based on HMM consensus sequences perform equivalently to HMMs that were adjusted to have constant gap transition probabilities, albeit with much greater variance. We observed no effect of composition-specific gap costs on retrieval performance. These results suggest possible improvements to the PSI-BLAST protein database search program.
  
  
  BACKGROUND
  The scripts for performing evaluations are available upon request from the authors.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
authors.forename: Aleksandar
authors.initials: A
authors.lastname: Stojmirović
authors.forename: E Michael
authors.initials: EM
authors.lastname: Gertz
authors.forename: Stephen F
authors.initials: SF
authors.lastname: Altschul
authors.forename: Yi-Kuo
authors.initials: YK
authors.lastname: Yu
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001185:Artificial Intelligence; D008390:Markov Chains; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods*; D011506:Proteins / Q000737:chemistry*; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D011506:Proteins