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Extracting Indels from two aligned DNA sequences

How i can extract Indels out from two aligned DNA sequences using python or biopython?

alignment
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updated by Hussain Ather Hussain Ather • written by manishagupta293 • manishagupta293

1 answer

SeqFIRE does what you want https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394284/

Otherwise you could use samtools view to view them.

samtools view -h in.bam  \
| awk '$1 ~ "^@" || $6 ~ "I|D"' \
| samtools view -b - > out.bam
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written by Hussain Ather Hussain Ather

SeqFIRE use protein alignments. But we want to use DNA alignment only. Is their a way to extract indels using BioPython?

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written by manishagupta293 • manishagupta293

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