Computational protocol: Evolution of bopA Gene in Burkholderia: A Case of Convergent Evolution as a Mechanism for Bacterial Autophagy Evasion

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Protocol publication

[…] All genomic sequences of Burkholderia strains and BopA gene sequences were downloaded from the NCBI database. Then a homologous search of BopA was conducted using the K96243 BopA protein sequence (accession number YP_111530.1N) against the NCBI nr protein sequence database using NCBI-BLAST online version. Meanwhile, PSI-BLAST was employed to the domain searching using the domain sequences of BopA as queries. The multiple sequence alignment was implemented by Muscle. [...] The motif prediction was conducted using online Eukaryotic Linear Motif database (http://elm.eu.org). All the predicted motifs were shown in logo that was generated by WebLogo 3 with default parameters (http://weblogo.berkeley.edu/logo.cgi). […]

Pipeline specifications

Software tools BLASTN, BLASTP, MUSCLE, BaMM!motif, WebLogo
Applications Nucleotide sequence alignment, Genome data visualization
Organisms Burkholderia pseudomallei