Computational protocol: Genome-Wide Comparative In Silico Analysis of the RNA Helicase Gene Family in Zea mays and Glycine max: A Comparison with Arabidopsis and Oryza sativa

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Protocol publication

[…] The helicase sequences were aligned using the ClustalX program with BLOSUM30 as the protein-weight matrix. The MUSCLE program (version 3.52) was also used to perform multiple sequence alignments to confirm the ClustalX results (http://www.clustal.org/) . Phylogenetic trees of the helicase protein sequences were constructed using the neighbour-joining (NJ) method of the MEGA5 program (http://www.megasoftware.net/) using the p-distance and complete deletion option parameters . The reliability of the obtained trees was tested using a bootstrapping method with 1000 replicates. The images of the phylogenetic trees were drawn using MEGA5. [...] Microarray expression data from various datasets were obtained using Genevestigator (https://www.genevestigator.com/gv/) with the Arabidopsis (ATH1∶22 k array), Oryza sativa (OS_51 k: Rice Genome 51 k array), Zea mays (ZM_84 k: Nimblegen Maize 385 k) and Glycine max (GM_60 k: Soybean Genome Array) Gene Chip platform. Then, the identified helicase-containing gene IDs were used as query sequences to perform searches in the Gene Chip platform of Genevestigator. […]

Pipeline specifications

Software tools Clustal W, MUSCLE, MEGA, Genevestigator
Applications Phylogenetics, Transcription analysis, Nucleotide sequence alignment
Organisms Zea mays, Glycine max, Arabidopsis thaliana, Oryza sativa