Binary Repeat Align serverby Lars Arvestad and Peter SavolainenAt this site you find software and an online service for aligning tandem repeat regions for which the repeats can be treated as marked by mutations. IntroductionTandem repeat regions are abundant in many genomes. Normally not very informative, except for various fingerprinting techniques using length statistics, regions where the repeats are marked, that is, there are slight variations of the basic repeat, remarkable patterns can occur. These patterns can be utilized for evolutionary analysis, as has been demonstrated in (Savolainen et al, 2000a), and forensic analysis (Savolainen et al, 2000b).Tandem repeats are believed to arise mainly from replication slippage, which causes repeats to be duplicated: A subsequence is copied twice during replication and the twin copies are found next to each other in the product. To take advantage this evolutionary artifact, we wrote two special computer programs. Available servicesThe web service is out-of-service at this point. Please contact Lars Arvestad if you are interested in this service!
SoftwareThe software, intended for Unix systems, is available under the GNU General Public License. It contains code for two programs,bra and
mcbra. The former computes a simple global alignment
under the mentioned restrictions, and the latter performs a
Mother-Child alignment.
Simple instructions are available using the '-u' option.
Download from here.
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