Computational protocol: Partial functional conservation of IRX10 homologs in physcomitrella patens and Arabidopsis thaliana indicates an evolutionary step contributing to vascular formation in land plants

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Protocol publication

[…] The Physcomitrella patens subsp patens v1.1 database and the Phytozome Physcomitrella database (http://www.phytozome.net/physcomitrella.php) were used to search for homologs using the Arabidopsis IRX10, IRX10-L, IRX9, IRX9-L, IRX14, IRX14-L, IRX8, PARVUS, GUX1 and GUX2 proteins. Sequences were aligned using Clustal-W software. Phylogenetic trees (Figure ) were computed using the neighbour-joining method [] as implemented in the Clustal-X software. The Phobius signal peptide and transmembrane prediction software was used for topological analysis (phobius.sbc.su.se) [,]. […]

Pipeline specifications

Software tools Clustal W, Phobius
Databases Phytozome
Application Phylogenetics
Organisms Arabidopsis thaliana, Physcomitrella patens
Chemicals Xylose