User: bethpearson98

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Posts by bethpearson98

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Count how many gaps and mismatches using pairwise2 alignment
... I am doing a local alignment using pairwise2. I currently have some code that will count how many matches there are but I am trying to also count how many gaps and mismatches there are in the alignment too. Is there any way to do this? If possible I'd like the gaps and mismatches counted separately ...
alignment sequence written 3 days ago by bethpearson980 • updated 2 days ago by Markus230
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Comment: C: Searching for a sequence within another sequence Biopython
... I have something like this atm but the sequences from the plasmids are very error prone and so it is unlikely that the main sequence will contain the sub sequence exactly. I was trying to use pairwise to get the alignment score but it I'm not sure how to get it to find a point in the first sequence ...
written 8 days ago by bethpearson980
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Searching for a sequence within another sequence Biopython
... I want to search for a recognition site sequence within another plasmid sequence. Currently I am trying to use pairwise2 local alignment but I am not sure what parameters to use. For instance, the plasmid seuqnce is something like: AGTGTTAAGAAGTCCGT and the recognition site is somwthing like: ...
alignment sequence written 9 days ago by bethpearson980 • updated 6 days ago by jrj.healey11k

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