Question: Extracting Indels from two aligned DNA sequences
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gravatar for manishagupta293
22 months ago by
manishagupta2930 wrote:

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

alignment • 579 views
ADD COMMENTlink modified 22 months ago by Hussain Ather940 • written 22 months ago by manishagupta2930
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gravatar for Hussain Ather
22 months ago by
Hussain Ather940
National Institutes of Health, Bethesda, MD
Hussain Ather940 wrote:

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
ADD COMMENTlink modified 22 months ago • written 22 months ago by Hussain Ather940

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

ADD REPLYlink written 22 months ago by manishagupta2930
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