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?
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Searching genome with specifed number of Ns between two known sequences
Started by seanspotatobusiness, Jan 16 2012 01:37 AM
2 replies to this topic
#2
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Guitar Hero
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... 
"When there's no more room in hell the dead will walk the Earth"
#3
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Epigenetist
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
