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Discontinuous/non-sequential sequences - (Apr/12/2013 )

Good evening!

I am searching for a way to analyse sequence-reads that contain blocks of sequence from 2 (or more) different genomic regions i.e.:

Genomic Region 1
Genomic Region 2

Any amount of the genome could theoretically reside between the two regions that were ligated to create this fragment.

Does anybody know of any software/program which will identify from where in the genome each block originated or have any suggestions on how I could accomplish this?

Many thanks for any help!



If it is one of the commonly studied organisms you could try UCSC's BLAT tool. BLAST might work, but would probably need more sequence than you have provided.