Computational protocol: The complete mitochondrial genome of the common sea slater, Ligia oceanica (Crustacea, Isopoda) bears a novel gene order and unusual control region features

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Protocol publication

[…] The alignment of the fragments to complete the whole mitochondrial DNA sequence was done in BioEdit 7.0.5.2 []. Each partial sequence was ascertained twice at least to prevent sequencing faults. Ambiguous base pairs were validated manually referring to chromatograms. Gene identification was determined by BLAST search on GenBank databases [] and by comparison to the mitochondrial Genome of Drosophila yakuba (NC001322). Boundaries of the protein coding genes were determined with a multiple alignment of other crustacean amino acid sequences. It was assumed that they were specified by the first start and stop codons in frame. Transfer RNA genes were determined with tRNAscan-SE 1.21 [] or by eye inspection for anti-codon sequences and secondary structures in regions between identified genes. Hairpin structures in non-coding regions were also identified by eye inspection. The control region and RNA genes were assumed to extend to adjacent genes, due to the lack of resources for a better determination of their boundaries. Nucleotide frequencies of protein coding and RNA genes were calculated with the DAMBE software package [], effective number of codons was determined according to [] with INCA 1.20 []. The complete genome sequence is submitted to NCBI GenBank [GenBank:DQ442914]. […]

Pipeline specifications

Software tools BioEdit, tRNAscan-SE, DAMBE
Applications Genome annotation, Phylogenetics