PipeAlign: A new toolkit for protein family analysis

Frádáric Plewniak; Laurent Bianchetti; Yann Brelivet; Annaick Carles; Frádáric Chalmel; Odile Lecompte; Thiebaut Mochel; Luc Moulinier; Arnaud Muller; Jean Muller; Veronique Prigent; Raymond Ripp; Jean Claude Thierry; Julie D. Thompson; Nicolas Wicker; Olivier Poch

doi:10.1093/nar/gkg518

PipeAlign: A new toolkit for protein family analysis

Frádáric Plewniak, Laurent Bianchetti, Yann Brelivet, Annaick Carles, Frádáric Chalmel, Odile Lecompte, Thiebaut Mochel, Luc Moulinier, Arnaud Muller, Jean Muller, Veronique Prigent, Raymond Ripp, Jean Claude Thierry, Julie D. Thompson, Nicolas Wicker, Olivier Poch^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Research › peer-review

106 Citations (Scopus)

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/.

Original language	English
Pages (from-to)	3829-3832
Number of pages	4
Journal	Nucleic Acids Research
Volume	31
Issue number	13
DOIs	https://doi.org/10.1093/nar/gkg518
Publication status	Published - 1 Jul 2003
Externally published	Yes

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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/.",

author = "Fr{\'a}d{\'a}ric Plewniak and Laurent Bianchetti and Yann Brelivet and Annaick Carles and Fr{\'a}d{\'a}ric Chalmel and Odile Lecompte and Thiebaut Mochel and Luc Moulinier and Arnaud Muller and Jean Muller and Veronique Prigent and Raymond Ripp and Thierry, {Jean Claude} and Thompson, {Julie D.} and Nicolas Wicker and Olivier Poch",

note = "Funding Information: This work was supported by funds from the Institut National de la Sant{\'e} et de la Recherche M{\'e}dicale, the Centre National de la Recherche Scientifique, the H{\^o}pital Universitaire de Strasbourg and the Fond National de la Science (GENOPOLE).",

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AU - Plewniak, Frádáric

AU - Bianchetti, Laurent

AU - Brelivet, Yann

AU - Carles, Annaick

AU - Chalmel, Frádáric

AU - Lecompte, Odile

AU - Mochel, Thiebaut

AU - Moulinier, Luc

AU - Muller, Arnaud

AU - Muller, Jean

AU - Prigent, Veronique

AU - Ripp, Raymond

AU - Thierry, Jean Claude

AU - Thompson, Julie D.

AU - Wicker, Nicolas

AU - Poch, Olivier

N1 - Funding Information: This work was supported by funds from the Institut National de la Santé et de la Recherche Médicale, the Centre National de la Recherche Scientifique, the Hôpital Universitaire de Strasbourg and the Fond National de la Science (GENOPOLE).

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PipeAlign: A new toolkit for protein family analysis

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