title: Automat and BLAST: comparison of two protein sequence similarity search programs.
abstract: Since the early 1980s, protein/DNA sequence similarity search has become of major importance to biologists, and the need for fast and efficient tools grows with the size of databanks. Two programs use the strategy of finite state deterministic automatons to accomplish these searches. One of these two is BLAST, which is now widely used, and the other Automat, which has just been published. The differences and similarities in their basic principles, their use and their performances are analysed in this paper in order to allow optimal use of these important softwares.
authors.affiliation: Laboratoire de Physiologie Cellulaire, Université P. et M. Curie, Paris, France.
authors.forename: H
authors.initials: H
authors.lastname: Cantalloube
authors.forename: G
authors.initials: G
authors.lastname: Labesse
authors.forename: J
authors.initials: J
authors.lastname: Chomilier
authors.forename: C
authors.initials: C
authors.lastname: Nahum
authors.forename: Y Y
authors.initials: YY
authors.lastname: Cho
authors.forename: V
authors.initials: V
authors.lastname: Chams
authors.forename: A
authors.initials: A
authors.lastname: Achour
authors.forename: A
authors.initials: A
authors.lastname: Lachgar
authors.forename: J P
authors.initials: JP
authors.lastname: Mbika
authors.forename: W
authors.initials: W
authors.lastname: Issing
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D016208:Databases, Factual; D005069:Evaluation Studies as Topic; D006801:Humans; D008969:Molecular Sequence Data; D011506:Proteins / Q000235:genetics*; D016415:Sequence Alignment / Q000706:statistics & numerical data*; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins