title: Multiple sequence alignment with user-defined constraints at GOBICS.
abstract: Most multi-alignment methods are fully automated, i.e. they are based on a fixed set of mathematical rules. For various reasons, such methods may fail to produce biologically meaningful alignments. Herein, we describe a semi-automatic approach to multiple sequence alignment where biological expert knowledge can be used to influence the alignment procedure. The user can specify parts of the sequences that are biologically related to each other; our software program uses these sites as anchor points and creates a multiple alignment respecting these user-defined constraints. By using known functionally, structurally or evolutionarily related positions of the input sequences as anchor points, our method can produce alignments that reflect the true biological relationships among the input sequences more accurately than fully automated procedures can do.
authors.affiliation: Institut für Mikrobiologie und Genetik, Universität Göttingen, Abteilung für Bioinformatik Goldschmidtstrasse 1, D-37077 Göttingen, Germany. burkhard@gobics.de
authors.forename: Burkhard
authors.initials: B
authors.lastname: Morgenstern
authors.forename: Nadine
authors.initials: N
authors.lastname: Werner
authors.forename: Sonja J
authors.initials: SJ
authors.lastname: Prohaska
authors.forename: Rasmus
authors.initials: R
authors.lastname: Steinkamp
authors.forename: Isabelle
authors.initials: I
authors.lastname: Schneider
authors.forename: Amarendran R
authors.initials: AR
authors.lastname: Subramanian
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.forename: Jan
authors.initials: J
authors.lastname: Weyer-Menkhoff
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D011506:Proteins / Q000032:analysis / Q000737:chemistry* / Q000145:classification*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins