Computational protocol: The GmFAD7 gene family from soybean: identification of novel genes and tissue-specific conformations of the FAD7 enzyme involved in desaturase activity

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Protocol publication

[…] The DFCI (Dana Faber Cancer Institute) database was used for BLAST searches of soybean sequences with homology to the previously annotated GmFAD7 gene sequence (GenBank accession no. L22965). Protein alignment was performed using the ClustalW Multiple alignment (BioEdit 7.0.9.0 software). Phylogenetic trees were generated using the PHYML software (; ww.atgc-montpellier.fr/PHYML) with bootstraps 500. Compute pI/Mw (ExPASy Server; http://www.expasy.ch/tools/pi_tool.html) was used for the theoretical pI (isoelectric point) and MW (molecular weight) calculation. The presence of a chloroplast transit peptide together with the prediction of subcellular localization was performed with ChloroP, pSORT, and TargetP analysis tools. The complete genomic sequence from soybean has recently been made available to the public at www.phytozome.net/soybean.php, (). […]

Pipeline specifications

Software tools Clustal W, BioEdit, PhyML, ChloroP, PSORT, TargetP
Databases ATGC Phytozome ExPASy
Applications Phylogenetics, Protein sequence analysis
Organisms Glycine max
Chemicals Iron