I'm supplementing an already published genetic database with genes extracted from full mitochondrial genomes from genbank. I have all accession numbers for the complete genomes and I have previous gene sequences too.
I'm using R to do all the downloading and data management but i'm willing to use other open access tools to do the job. So far, my plan is to just download the full genome, replicate it in separate fasta files for each mitochondrial gene, align all the sequences for that specific gene and then trim sequences manually. I could also go genome by genome extracting the genes manually on genbank, but I figure there is a smarter and quicker way to do it.
I have never done anything like this, so I'm playing by ear here. Any tips are welcome.
Olá Fabio, your current plan of downloading complete genomes, then get the mitogenomes, and then select whatever DNA segments you are interested in via trimming might work well and should not be as painful as it sounds if you use Geneious. I know you are searching for a free-of-charge option, but I anyway wanted to let you know that this program would make your task relatively easy (WAY easier than in Mesquite, MEGA, etc). Also, a couple of days ago I saw that a new R package was released and, I think,it does exactly what you want to do. I will confirm this info and get its name and let you know.
Found it: "AnnotationBustR: An R package to extract subsequences from GenBank annotations" Here: https://peerj.com/preprints/2920.pdf
Eliecer, thanks!
I've heard of Geneious, but unfortunately I am, at the present moment, without fundings to acquire it. So free softwares will have to do. I will check O'Meara's package. It looks like the thing for me now.
It did the trick wonderfully! However, it uses genbank annotations to find the genes and extract them. That left me with only one genome that will have to be processed "by hand". In anyway, it was very helpful.
Saludos!
It did the trick wonderfully! However, it uses genbank annotations to find the genes and extract them. That left me with only one genome that will have to be processed "by hand". In anyway, it was very helpful.
Saludos!
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