blastn for short intergenic sequences

[Barbara MacGregor]

Hello IMG users,

I hope there's an obvious solution here that I'm just not seeing. I am searching many species for a repeated 7-mer nucleotide sequence that is usually intergenic. Searching GenBank with 7 tandem copies of this, the parameters are magically adjusted for short input sequences, and I get a nice long list of hits. Ideally, I would like to do the same thing in IMG/ER, in order to investigate the gene neighborhoods, but don't see how or where.

Failing that, I would like to use the GenBank results to search IMG/ER, but here again I don't see a straightforward way. Because the sequences are intergenic, the gi and accession number hit lists are for entire genomes or contigs. The aligned sequences are of course all too short to work for IMG/ER searches. And doing it by hand from dozens of genomes, well, I have a lot of patience but eventually there's a limit.

I can look at gene neighborhoods in GenBank of course, but that's much clumsier (at least in my hands).

Thanks for any help,

Barbara

[Ernest Szeto]

You will probably have to do this offline.  The closest we have is in the download tar bundle, a file with the precomputed with intergenic regions > 10bp.   You can use this file to generate a BLASTN database and run it with the appropriate parameters offline to see  if you get anything interesting.