Computational protocol: Identification and Characterization of RcMADS1, an AGL24 Ortholog from the Holoparasitic Plant Rafflesia cantleyi Solms Laubach (Rafflesiaceae)

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Protocol publication

[…] The PCR products were purified using the QIAquick® PCR purification kit (QIAGEN) following the manufacturer’s instructions. The purified PCR product was cloned into the pGEM®-T Easy Vector (Promega). Selected clones were sequenced via an automated sequencing method using ABI PRISM™ Big Dye™ Terminator Cycle Sequencing Ready Reaction Kit (Applied Biosystems). Sequences obtained after automated sequencing were collated and compared with published sequences in the GenBank database using the Basic Local Alignment Search Tool (BLAST) program on the National Center for Biotechnology Information (NCBI) website. The algorithms used were blastn (to search the nucleotide database using a nucleotide query) and tblastx (to search the translated nucleotide database using a translated nucleotide query). [...] Phylogenetic analysis was performed using the Phylogeny.fr online software (http://www.phylogeny.fr/version2_cgi/simple_phylogeny.cgi) with one click mode, where MUSCLE, Gblocks, PhyML, and TreeDyn programs were used for multiple alignment, curation, tree building and tree rendering, respectively . […]

Pipeline specifications

Software tools BLASTN, TBLASTX, Phylogeny.fr, Gblocks, PhyML, TreeDyn
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Arabidopsis thaliana