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

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

alignment • 285 views
ADD COMMENTlink modified 7 months ago by Hussain Ather880 • written 7 months ago by manishagupta2930
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gravatar for Hussain Ather
7 months ago by
Hussain Ather880
National Institutes of Health, Bethesda, MD
Hussain Ather880 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 7 months ago • written 7 months ago by Hussain Ather880

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

ADD REPLYlink written 7 months ago by manishagupta2930
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