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Searching genome with specifed number of Ns between two known sequences


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#1 seanspotatobusiness

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Posted 16 January 2012 - 01:37 AM

Do you know if there's a way to search a genome in BLAST for sequences separated by, say, 5-30 N? E.g. AAAA (N)5-30 TTTT?

#2 toejam

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Posted 16 January 2012 - 07:53 AM

just input your sequence. i'd use global alignment rather than local for that kind of purpose. at least i believe so... it's been over 4 years since i did proper bioinformatics... Posted Image
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#3 pcrman

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Posted 16 January 2012 - 04:56 PM

Yes, you can just insert nnnnnnn into your query sequence. Try BLAT http://genome.ucsc.edu/cgi-bin/hgBlat




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