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PipeAlign: a new toolkit for protein family analysis

F. Plewniak
2003 Nucleic Acids Research  
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  ...  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.  ...  As a consequence, a new generation of protein family analysis tools is now required to organise this heterogeneous, often predicted data into a structured, hierarchical network of connected information  ... 
doi:10.1093/nar/gkg518 pmid:12824430 pmcid:PMC168925 fatcat:vmvodzvwtndqjdh5nczivu2cbq

GOAnno: GO annotation based on multiple alignment

F. Chalmel, A. Lardenois, J.D. Thompson, J. Muller, J.-A. Sahel, T. Leveillard, O. Poch
2005 Bioinformatics  
Availability: The web tool and a reduced version for local installation are freely available at  ...  GOAnno is a web tool that automatically annotates proteins according to the Gene Ontology (GO) using evolutionary information available in hierarchized multiple alignments.  ...  Ripp for stimulating discussions.  ... 
doi:10.1093/bioinformatics/bti252 pmid:15647299 fatcat:bc2tf54usjav3i2basjqkrp2me

A new protein linear motif benchmark for multiple sequence alignment software

Emmanuel Perrodou, Claudia Chica, Olivier Poch, Toby J Gibson, Julie D Thompson
2008 BMC Bioinformatics  
As a consequence, poor motif alignment quality is hindering efforts to detect new LMs.  ...  Methods for LM detection are now being developed that are strongly dependent on scores for motif conservation in homologous proteins.  ...  Acknowledgements We would like to thank the Bioinformatics Platform of Strasbourg (BIPS), Jean-Claude Thierry and Dino Moras for their support.  ... 
doi:10.1186/1471-2105-9-213 pmid:18439277 pmcid:PMC2374782 fatcat:eukbqcn4prdmfmj5m47q6lhnj4

Structure Based Protein Multiple Sequence Alignment Algorithm on a Parallel System

Muhammad Ishaq Afridi, Yin Gui Sheng
2012 International Journal of Machine Learning and Computing  
Index Terms-APDB (A with PDB is used for ADP), BLAST, Cluster based on Mesh topology, DLT (Divisible load theory), FASTA, expresso, MPICH-G2, MPICH, PipeAlign, PRALINE, RMSD, Structure based Protein MSA  ...  To enhance the speed and efficiency of structure based algorithms for protein Multiple Sequence alignment we need parallel processing.  ...  and structure of Protein 2 A new toolkit for protein family analysis 3 Search protein databases at NCBI and is faster than BLASTN by applying novel sequence similarity method. restricting the output  ... 
doi:10.7763/ijmlc.2012.v2.86 fatcat:wm6kclvy45aq5phq75pqzmx7s4

Insights into metazoan evolution from alvinella pompejana cDNAs

Nicolas Gagnière, Didier Jollivet, Isabelle Boutet, Yann Brélivet, Didier Busso, Corinne Da Silva, Françoise Gaill, Dominique Higuet, Stéphane Hourdez, Bernard Knoops, François Lallier, Emmanuelle Leize-Wagner (+13 others)
2010 BMC Genomics  
Analysis of more than 75,000 high quality reads led to the identification of 15,858 transcripts and 9,221 putative protein sequences.  ...  Alvinella proteins seem to show a slow evolutionary rate and a higher similarity with proteins from Vertebrates compared to proteins from Arthropods or Nematodes.  ...  Acknowledgements We wish to acknowledge Julie Thompson for a critical reading of the manuscript and Marc Robinson-Rechavi for fruitful discussions.  ... 
doi:10.1186/1471-2164-11-634 pmid:21080938 pmcid:PMC3018142 fatcat:zxsmif3y7nhx3g2sfnei473kxy

AlexSys: a knowledge-based expert system for multiple sequence alignment construction and analysis

M. R. Aniba, O. Poch, A. Marchler-Bauer, J. D. Thompson
2010 Nucleic Acids Research  
Here, we describe the development of a new expert system, AlexSys, for the multiple alignment of protein sequences.  ...  Applying AlexSys to a test set of 178 alignments, we show that the expert system represents a good compromise between alignment quality and running time, making it suitable for high throughput projects  ...  Platform (BIPS) for their support.  ... 
doi:10.1093/nar/gkq526 pmid:20530533 pmcid:PMC2965243 fatcat:ugzgjval5va4vp5d6ztvvl5yp4

Conjugating effects of symbionts and environmental factors on gene expression in deep-sea hydrothermal vent mussels

Isabelle Boutet, Raymond Ripp, Odile Lecompte, Carole Dossat, Erwan Corre, Arnaud Tanguy, François H Lallier
2011 BMC Genomics  
Among all these genes, those participating in recognition, the immune system, oxidative stress, and energy metabolism constitute new promising targets for extended studies on symbiosis and the effect of  ...  Microarray analysis showed that 120 genes (3.5% of all genes) were differentially expressed between the Menez Gwen (MG) and Rainbow (Rb) vent fields.  ...  We thank Isabelle Guisle and the Plateforme Puces à ADN (Biogenouest ® , Nantes, France) for microarray printing.  ... 
doi:10.1186/1471-2164-12-530 pmid:22034982 pmcid:PMC3218092 fatcat:wseirl3wtbcavorwggwq2oiele

On computational strategies for regulatory element and regulatory polymorphism detection

Stephen Blair Montgomery
Integrating and assessing this information remains a major scientific endeavor that requires new and innovative application of technology.  ...  Regulatory variants are thought to be responsible for a considerable amount of the heterogeneity within our population and to be fundamental determinants of health.  ...  Vatcher, personal communication). 4) SARS-CoV phylogeny: Using data generated from a BLASTX analysis of the protein complement of the nidovirales family against the SARS-CoV virus, Sockeye was able to  ... 
doi:10.14288/1.0093020 fatcat:tl6tplfc2zbsvbefqb3olizea4