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find a sequence that may be gapped with other characters
2013-12-01
azim58 - find a sequence that may be gapped with other characters search for a special regex version of the sequence you want in a program that can handle regex find and replex For example, say you want to find the sequence TTGATACCACTGCTT in this subject sequence GGGGTAC:GATGAGATTG:ATACCACTGCTTGGGATCCTCTAGAGTC change this sequence TTGATACCACTGCTT into T(:+)?T(:+)?G(:+)?A(:+)?T(:+)?A(:+)?C(:+)?C(:+)?A(:+)?C(:+)?T(:+)?G(:+)?C(: +)?T(:+)?T(:+)? using find (\w) and replace $1(:+)? or $1\(:+\)? Then search the subject sequence GGGGTAC:GATGAGATTG:ATACCACTGCTTGGGATCCTCTAGAGTC with the query sequence T(:+)?T(:+)?G(:+)?A(:+)?T(:+)?A(:+)?C(:+)?C(:+)?A(:+)?C(:+)?T(:+)?G(:+)?C(: +)?T(:+)?T(:+)?
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