Computational protocol: The Aeromonas salmonicida Lipopolysaccharide Core from Different Subspecies: The Unusual subsp. pectinolytica

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Protocol publication

[…] For each analyzed genome we gathered all CDS and pseudo-CDS information by parsing NCBI GenBank records. When we obtained the UniProt Knowledge Base records for these loci using the cross-reference with Entrez GeneIDs and parsed them for gene names, functional annotations, and associated COG, PFAM, and TIGRFAM protein domains were studied. To annotate orthologs, we wrote custom scripts to analyze reference sequence alignments made to subject genomes with blastn and tblastn via NCBI’s Web application programming interface. Briefly, we manually confirmed contextually accurate alignments, and then the script integrated coordinates and sequence information from both BLAST methods to locate the bounds of the reference gene in the subject genome; if an aligned start or stop codon was not located, we manually inspected the region. The script then analyzed alignments for insertions, deletions, premature stop codons, frameshifts, and changes to the start codon. An alignment in the same genomic context with >95% amino acid identity, excluding gaps and truncations, was our initial cutoff for orthology. The genomes of subsp. salmonicida A449, subsp. masoucida strain NBRC13784, subsp. achromogenes strain AS03 and subsp. pectinolytica strain 34melT are located at the GenBank accession numbers: CP000644, BAWQ00000000, AMQG00000000.2 and ARYZ00000000.2, respectively. The complete nucleotide sequences of the three A. salmonicida A450 chromosomal regions containing the LPS core biosynthetic genes described here have been assigned GenBank accession numbers FJ238464, FJ238465, and FJ238466, respectively. The complete nucleotide sequences of the three A. hydrophila AH-3 chromosomal regions containing LPS core biosynthesis genes described here have been assigned the following GenBank accession numbers: EU296246, EU296247, and EU296248. […]

Pipeline specifications

Software tools BLASTN, TBLASTN
Databases Pfam
Applications Phylogenetics, Amino acid sequence alignment
Organisms Aeromonas salmonicida
Chemicals Galactose