title: Issues in searching molecular sequence databases.
abstract: Sequence similarity search programs are versatile tools for the molecular biologist, frequently able to identify possible DNA coding regions and to provide clues to gene and protein structure and function. While much attention had been paid to the precise algorithms these programs employ and to their relative speeds, there is a constellation of associated issues that are equally important to realize the full potential of these methods. Here, we consider a number of these issues, including the choice of scoring systems, the statistical significance of alignments, the masking of uninformative or potentially confounding sequence regions, the nature and extent of sequence redundancy in the databases and network access to similarity search services.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894.
authors.forename: S F
authors.initials: SF
authors.lastname: Altschul
authors.forename: M S
authors.initials: MS
authors.lastname: Boguski
authors.forename: W
authors.initials: W
authors.lastname: Gish
authors.forename: J C
authors.initials: JC
authors.lastname: Wootton
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D016208:Databases, Factual; D006801:Humans; D016247:Information Storage and Retrieval; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D017385:Sequence Homology; D012984:Software