hello there, many of us around our labs use Artemis and ACT with moderate frequency, however I'm up against an Artemis weirdness that no one around here can explain to me; so I'm helping you folks can!
In the Comparison View Pop-up Menu, it is possible to Set the Percent ID cutoffs. This slides from 0% to 100%, and the default view is 0%. If I have my match-size set at, say, 70 bp, what does it mean for the % identity to be 0?? Logically, there's a 1-in-4 chance that a single base would match another base, so it seems like for anything 4bp or longer the true default identity cutoff would be, say, 25%. Or if the cutoff is 50%, does that really mean that what I'm seeing represented in Comparison View is 70-mers that share at least 35bp with their matches? The more I think about this the more I think it's merely a BLAST-weirdness, not an Artemis one. What this % identity is really letting the user select is just the % identity within whatever *aligned* sequences are present in the BLAST match between the two genomes, and thus is not a particularly meaningful way to look, for example, at 80% IDENTICAL 70-MERS ACROSS TWO GENOMES (this really being my goal). This is likely better achieved by determining what the e-value for such a match across a 70-mer would be given these two genomes, and using that to Set the Score Cutoff. Would you folks agree with this interpretation, and/or would you have any suggestions for a better way to visualize genome comparisons via 70mers with varying percents of identity? Thanks a lot! Virginia Rich ~~~~~~~~~~~~~~~~~~~ Virginia Rich [EMAIL PROTECTED] DeLong Lab MIT _______________________________________________ Artemis-users mailing list [email protected] http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
