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Old 07-17-2014, 10:01 AM   #1
helelein
Junior Member
 
Location: paris

Join Date: Jul 2014
Posts: 3
Default How to blast a transposon sequence to a MiSeq transposon library

Hi there!
I'm brand new on the forum and in massive parallel sequencing analysis too!

I have sequenced 2 transposon libraries from a bacterial genome (input/output pool) with MiSeq from Illumina. My interest is to find where the transposon has been inserted in the bacterial genome. For the sequencing, DNA was broken into small pieces and transposon containing fragments were captured with a biotinilated probe.

Before blasting my transposon sequences to the bacterial genome, I need to check my sequences and get rid of the ones that don't have it. Therefore I would like to make a blast of my sequences or align them with the end of the sequence of the transposon; in order to get rid of the sequences not containing the transposon.

Could anyone give me a hint how to perform such a blast, please? I'm trying with CLC workbench but don't manage to do it. Since usually a blast is done against a database and I just want to blast a single sequence.

Thanks!
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