CSA: Comprehensive comparison of pairwise protein structure alignments

Inken Wohlers; Noël Malod-Dognin; Rumen Andonov; Gunnar W. Klau

hal-00667920, version 1

CSA: Comprehensive comparison of pairwise protein structure alignments

Inken Wohlers ( Auteur à contacter de préférence )^b^, 1, Noël Malod-Dognin () ², Rumen Andonov ()^a^, 3, Gunnar W. Klau ()^b^, 1

Nucleic Acids Research (2012) 303-309

Résumé : CSA is a web server for the comprehensive comparison of pairwise protein structure alignments. Its exact alignment engine computes either optimal, top-scoring alignments or heuristic alignments with quality guarantee for the inter-residue distance based scorings of contact map overlap, PAUL, DALI and MATRAS. These and additional, uploaded alignments are compared using a number of quality measures and intuitive visualizations. CSA brings new insight into the structural relationship of the protein pairs under investigation and is a valuable tool for studying structural similarities. It is available at http://csa.project.cwi.nl

a – Université de Rennes I
b – CWI
1 : Life Sciences (MAC4)
Centrum Wiskunde & Informatica
2 : ABS (INRIA Sophia Antipolis)
INRIA
3 : GENSCALE (INRIA - IRISA)
INRIA – CNRS : UMR6074 – Université de Rennes 1 – École normale supérieure de Cachan - ENS Cachan

Collaboration : Life Sciences, Centrum Wiskunde & Informatica, Science Park 123, 1098 XG Amsterdam, the Netherlands

hal-00667920, version 1
http://hal.inria.fr/hal-00667920
oai:hal.inria.fr:hal-00667920
Contributeur : Rumen Andonov <>
Soumis le : Lundi 13 Février 2012, 08:56:42
Dernière modification le : Lundi 17 Décembre 2012, 21:51:03

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arXiv : 1202.2670

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%F hal-00667920, version 1
%0 Journal Article
%U http://hal.inria.fr/hal-00667920
%2 INFO:INFO_BI;SDV:BIBS
%T CSA: Comprehensive comparison of pairwise protein structure alignments
%A Wohlers, Inken
%A Malod-Dognin, Noël
%A Andonov, Rumen
%A Klau, Gunnar W.
%+ Life Sciences - MAC4 , ABS - INRIA Sophia Antipolis , GENSCALE - INRIA - IRISA
%X CSA is a web server for the comprehensive comparison of pairwise protein structure alignments. Its exact alignment engine computes either optimal, top-scoring alignments or heuristic alignments with quality guarantee for the inter-residue distance based scorings of contact map overlap, PAUL, DALI and MATRAS. These and additional, uploaded alignments are compared using a number of quality measures and intuitive visualizations. CSA brings new insight into the structural relationship of the protein pairs under investigation and is a valuable tool for studying structural similarities. It is available at http://csa.project.cwi.nl
%2 CSA est un serveur web pour la comparaison compréhensible des alignements de paires de protéines. Son moteur d'alignement exact calcule, pour les scores de similarité basés sur les distances inter-résidus CMO (Contact Map Overlap maximization), PAUL, DALI et MATRAS, soit des alignements optimaux (ayant le plus haut score), soit des alignements heuristiques avec une garantie de qualité. Ces alignements, plus ceux uploadés par l'utilisateur, sont comparés en utilisant de nombreuses mesures de qualité et des visualisations intuitives. CSA apporte un nouveau regard sur les relations structurales entre paires de protéines, et constitue un outil précieux pour l'étude des similarités structurales. CSA est disponible sur http://csa.project.cwi.nl
%G Anglais
%J Nucleic Acids Research
%8 2012-00-00
%2 internationale
%I Oxford Journals
%2 40
%P 303-309
%2 Preprint, submitted to Nucleic Acids Research
%K Protein structure alignments; alignment comparison; web server; exact algorithm; scoring function
%Z Preprint, submitted to Nucleic Acids Research
%Z RR-7874
%Z DFG [KL 1390/2-1]
%Z Life Sciences, Centrum Wiskunde & Informatica, Science Park 123, 1098 XG Amsterdam, the Netherlands

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