title: PRALINE: a versatile multiple sequence alignment toolkit.
abstract: Profile ALIgNmEnt (PRALINE) is a versatile multiple sequence alignment toolkit. In its main alignment protocol, PRALINE follows the global progressive alignment algorithm. It provides various alignment optimization strategies to address the different situations that call for protein multiple sequence alignment: global profile preprocessing, homology-extended alignment, secondary structure-guided alignment, and transmembrane aware alignment. A number of combinations of these strategies are enabled as well. PRALINE is accessible via the online server http://www.ibi.vu.nl/programs/PRALINEwww/. The server facilitates extensive visualization possibilities aiding the interpretation of alignments generated, which can be written out in pdf format for publication purposes. PRALINE also allows the sequences in the alignment to be represented in a dendrogram to show their mutual relationships according to the alignment. The chapter ends with a discussion of various issues occurring in multiple sequence alignment.
authors.affiliation: Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, Amsterdam, The Netherlands.
authors.forename: Punto
authors.initials: P
authors.lastname: Bawono
authors.forename: Jaap
authors.initials: J
authors.lastname: Heringa
mesh_terms: D002462:Cell Membrane / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D020407:Internet; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D016415:Sequence Alignment / Q000379:methods*; D017385:Sequence Homology; D012984:Software
chemical_list: D011506:Proteins