How can we analyze the Sanger sequencing result for detecting indels or substitutions? Is pair-wise alignment enough for finding out indels or is any particular software available for finding the above?
Heterozygous indels are immediately obvious when looking at an electropherogram of the sequence when a good clean electropherogram becomes a complete mess of 2 overlapping sequences instantly but the peak heights are still strong. Homozygous indels can be detected with NCBIs BLAST programme or a;ignment software such as Sequencher or any similar pairwise alignment software
Hi Vidya
to complete Paul's answer, heterozygous states for indels can be a mess. the best way for Sanger sequencing to allow accurate indels detection is to get the cleanest sequence you can and for both sides to confirm positions and sequence.
all the best
fred
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