Computational protocol: Identification and characterization of MAGO and Y14 genes in Hevea brasiliensis

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Protocol publication

[…] Analysis and comparison of the HbMAGO and HbY14 sequences were done using BLAST at the NCBI database. Clustal X (http://www.ebi.ac.uk/clustalw) was used for multiple alignments of the nucleic acid and amino acid sequences of HbMAGOs and HbY14s. A phylogenetic tree was constructed with MEGA5.2 (http://www.megasoftware.net/) using the maximum likelihood (ML) method with a bootstrap parameter of 1000 replicates. The sequence information for a number of homologs from other species was retrieved from the NCBI database and is shown in the explanatory text of . Genomic structures of the HbMAGOs and HbY14s were analyzed by comparing the cDNA sequences using GSDS software (http://gsds.cbi.pku.edu.cn/) and the corresponding genomic DNA sequences that were extracted from the local whole genome shotgun database. […]

Pipeline specifications

Software tools Clustal W, MEGA, GSDS
Application Phylogenetics
Organisms Hevea brasiliensis, Salminus brasiliensis
Chemicals Amino Acids, NADP