Hi Phil, The X's signify that the query sequences has been put through a low complexity filter 'SEG' which will X out low complex sequences. These sequences may introduce false positives into the results. To turn the low complexity filter off use the -F F option. Assuming you're using the command line version of BLAST. Hope this helps Noel Phil Princely wrote: > Hi all, > > I'm new here, so sorry if this is a bit of an obvious question. I've > been using blast for a while now, but am still learning. Here's my > problem: > > I used formatdb to make a blast database from a text file with about > 2000 genes. Everything went well, and I could query the database. But > when I input a sequence from the original text file, the result isn't > always 100%. Sometimes it comes out 98% or 95%, when it should always > be 100%. When I look at the results, I find one or more series of xs, > signifying a missing part of data. For example: > > Score = 1815 bits (4702), Expect = 0.0 > Identities = 913/953 (95%), Positives = 913/953 (95%) > > LTLDRLSNTLSGGESQRISLATQXXXXXXXXXXXXDEPSIGLHQ (Query) > LTLDRLSNTLSGGESQRISLATQ DEPSIGLHQ > LTLDRLSNTLSGGESQRISLATQLGSSLVGSLYVLDEPSIGLHQ (Subject) > > Is there a way to make this 100%. I want to run the 2000 genes against > another genome to find 100% similar regions, 95% similar regions and > so on. > > Thanks > > Phil P > _______________________________________________ > Biodevelopers mailing list > Biodevelopers at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biodevelopers