Multiple sequence alignment of mtDNA HV1-3 in R

Question

[irieljoerin]

Hi all,

I would like to perform a multiple sequence alignment from a fasta file containing multiple mitogenomes (mitochondrial genomes). The problem is that some of them are complete linear sequences (mtDNA is circular), but others contain only hypervariable regions 1, 2, and 3 (HV1-3), which are at the end and at the beginning of the reference sequence, respectively. So, HV1-3 fasta sequences contain a gap (-) in the middle and they need to align at the end and at the beginning of the complete mitogenomes. Y tried to do that with msa function from msa package in R, but the HV1-3 sequence produced a wrong alignment. I need to align several sequences (both complete and only HV1-3) to convert the alignment to a matrix after that. Then I can perform other analyses. Can somebody advise me about a function to do that in r? I´ll appreciate your help very much! Best regards

Answer 1

[MatthewP]

I think you can try mode "einsi" of mafft to align your sequences, then use Biostrings::readDNAMultipleAlignment() to read alignments into R. You can use system() function in R to run shell command.

[irieljoerin]

Thank you MatthewP for your answer! Is there an option to do the same, but aligning multiple sequences to a reference?