Cenci, A.

Guignon, V.

Rouard, M.

English

Guignon, Valentin

CGSpace

Exchange your knowledge on plant gene familiesGuignon V1, Cenci A1, Rouard M11 Bioversity International - Commodity Systems & Genetic Resources Programme, Parc Scientifique Agropolis II, 34397Montpellier - Cedex 5, FranceGreenPhylABCDEFv4...but is there any repository?Many studies on plant gene families...What is GreenPhyl?A published public web resource designed forcomparative and functional genomics in plants:              ● 4th release              ● 37 complete plant genomes              ● 1 300 000 gene sequences              ● 8 300 sequence clusters              ● 2 900 annotated clustersGet started with GreenPhyl to add value to your gene families!                                                        ● easy gene family creation                                                        ● feature management                                                        ● nice displayb. Phylogeny analysis displayb. Building gene familyfrom FASTA sequencesFamily search?3. Displaya. Species composition2. Searchinga. Building gene familyfrom GreenPhyl data using"My List" featurestep 1: Multiple-FASTA importstep 2: Species validationABSTRACT: Every year, hundreds of gene families are characterized through peer-review publications but their structure and classification is hardlycaptured by dedicated databases such as Phytozome, Plaza, Ensembl or GreenPhylDB. To address this situation, we developed a user-friendlyinterface allowing either to customize pre-computed protein sequence clusters or to create new ones based on prior knowledge of a given gene family.Information can be then shared with collaborators and/or reviewers with a unique URL.1. RationaleExternal tools:GalaxyFamily directory c. (Sub)family    relationship4. Creationsupports all plant UniProtcodes (>4000 species)References:1. Cenci A, Guignon V, Roux N, Rouard M. Genomic analysis of NAC transcription factors in banana (Musa acuminata) and definition of NAC orthologous groups for monocots and dicots. Plant Mol Biol. 2014 Feb 26.2. Jourda, C., Cardi, C., Mbéguié-A-Mbéguié, D., Bocs, S., Garsmeur, O., D'Hont, A. and Yahiaoui, N. (2014), Expansion of banana (Musa acuminata) gene families involved in ethylene biosynthesis and signalling after lineage-specific whole-genome duplications. New Phytologist. doi: 10.1111/nph.12710.3. Rouard,M., Guignon,V., Aluome,C., Laporte,M.-A., Droc,G., Walde,C., Zmasek,C.M., Perin,C. et Conte,M.G. (2011) GreenPhylDB v2.0: comparative and functional genomics in plants. Nucleic Acids Research, 39, D1095-D1102, 10.1093/nar/gkq811.4. Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009), Jalview Version 2 - a multiple sequence alignment editor and analysis workbench. Bioinformatics25 (9) 1189-1191 doi: 10.1093/bioinformatics/btp0335.  Zmasek C.M., Eddy S.R. ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics. 2001, Apr;17(4):383-4."My List" is a clipboard-like space storing a set of sequences.This set can be modified using another set of selectedsequences or gene families by applying some basic operations:Free, required for gene family creation,OpenID supported: use your Google,Yahoo!, etc. account to log in!Merge ReplaceMy ListSelectionIntersect Substractoperationsto my listto galaxyto displayto displayto gene family managementto gene family managementdynamic edition5 access levels        restricted (read or read/edit)for publication review process, collaboration, ...         Public access(read or read/edit)for visibility orwiki-stylegene family        privatefor work in progressto displayc. Phylogeny analysisUser accountContent5. ManagementPropertiesAccess controlDesigned for peer-review processa. Sequence managementb. Relationship    management"private" URLor passwordd. Sequence export    and mappingto my list

Exchange your knowledge on plant gene families

https://cgspace.cgiar.org/bitstream/10568/67497/1/Guignon_exchangeyourknowledge.pdf

Exchange your knowledge on plant gene families

Abstract

Similar works

Full text

Available Versions

CGSpace