Identifying Long terminal repeats (LTRs) - (Nov/20/2007 )
I was hoping someone would be able to advise me on how to identify long terminal repeats. I'm in the process of designing primers to screen gDNA from clones which (hopefully) will contain a knockout. This is an alternative to Southern blotting (which has not been good to me!) I've been warned the region that I'm designing my forward primer will contain an LTR. I'm not sure how I can find where this starts and so avoid including it in the primer sequence. Are there any databases or search tools on the web I can use for this? I've tried downloading the "LTR-STRUCT" application but I keep generating error reports.
you can try repeatmasker for this (http://www.repeatmasker.org/cgi-bin/WEBRepeatMasker) this is a web application that will look not only for LTRs but also for LINES, SINEs and other repeats you should avoid in your primer design