title: PipeAlign: A new toolkit for protein family analysis.
abstract: PipeAlign is a protein family analysis tool integrating a five step process ranging from the search for sequence homologues in protein and 3D structure databases to the definition of the hierarchical relationships within and between subfamilies. The complete, automatic pipeline takes a single sequence or a set of sequences as input and constructs a high-quality, validated MACS (multiple alignment of complete sequences) in which sequences are clustered into potential functional subgroups. For the more experienced user, the PipeAlign server also provides numerous options to run only a part of the analysis, with the possibility to modify the default parameters of each software module. For example, the user can choose to enter an existing multiple sequence alignment for refinement, validation and subsequent clustering of the sequences. The aim is to provide an interactive workbench for the validation, integration and presentation of a protein family, not only at the sequence level, but also at the structural and functional levels. PipeAlign is available at http://igbmc.u-strasbg.fr/PipeAlign/.
authors.affiliation: Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, BP 10142, 67404 Illkirch Cedex, France.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Plewniak
authors.forename: Laurent
authors.initials: L
authors.lastname: Bianchetti
authors.forename: Yann
authors.initials: Y
authors.lastname: Brelivet
authors.forename: Annaick
authors.initials: A
authors.lastname: Carles
authors.forename: Frédéric
authors.initials: F
authors.lastname: Chalmel
authors.forename: Odile
authors.initials: O
authors.lastname: Lecompte
authors.forename: Thiebaut
authors.initials: T
authors.lastname: Mochel
authors.forename: Luc
authors.initials: L
authors.lastname: Moulinier
authors.forename: Arnaud
authors.initials: A
authors.lastname: Muller
authors.forename: Jean
authors.initials: J
authors.lastname: Muller
authors.forename: Veronique
authors.initials: V
authors.lastname: Prigent
authors.forename: Raymond
authors.initials: R
authors.lastname: Ripp
authors.forename: Jean-Claude
authors.initials: JC
authors.lastname: Thierry
authors.forename: Julie D
authors.initials: JD
authors.lastname: Thompson
authors.forename: Nicolas
authors.initials: N
authors.lastname: Wicker
authors.forename: Olivier
authors.initials: O
authors.lastname: Poch
mesh_terms: D020407:Internet; D011506:Proteins / Q000737:chemistry / Q000145:classification*; D011786:Quality Control; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software / Q000592:standards; D014584:User-Computer Interface
chemical_list: D011506:Proteins