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In these days, DNA sequences are first analyzed and protein sequences are translated from them, and consequently codon sequences are likely available for most protein sequences in databases.
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All longitudinal within-host sequences were translated from nucleotide to protein sequences with the GeneCutter tool (http://www.hiv.lanl.gov/content/sequence/HIV/HIVTools.html).html
The wild type protein sequences were translated from cDNA sequences obtained from HGMD.
Amino acid sequences were translated from coding sequences and aligned by BioEdit (6 ).
Protein sequences were translated from BAC clones or sequenced constructs using Expasy translate, and aligned by hand.
Also, 12, 11, and 9 protein sequences were translated from the haplotypes in S. officinarum, S. robustom, S. spontanuem, respectively.
The corresponding protein sequences were translated from the predicted transcripts with a minimum length requirement of eighteen amino acids.
After fasty/tfasty search, the peptide sequences were translated from assembled nucleotide contig/singleton sequences according to the alignment with their best Csl hits.
Then, to prepare the remaining sequences for the subsequent alignment, all coding mitochondrial sequences were translated from nucleotide to corresponding amino acid sequences with the aid of the script dna2aa, which uses the respective GenBank information for this task [b.V].
The peptide sequences were translated from assembled nucleotide contigs and singletons according to the fasty alignment with their best Csl hits, which are published Csl proteins previously classified into the 10 existing Csl families [ 27].
The western clawed frog Dpl sequence was translated from JGI4.1 scaffold_143 1604545:1605090 (Ensembl).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com