Denovo repeat finder: Difference between revisions

From genomewiki
Jump to navigationJump to search
No edit summary
 
(fix link to repeat masker)
 
(9 intermediate revisions by 4 users not shown)
Line 1: Line 1:
Currently there are a few choices for denovo repeat programs:
A '''denovo repeat finder''' is a program designed to find repeats in DNA sequence without using the [http://www.repeatmasker.org/ RepeatMasker] library. Currently there are a few choices for denovo repeat programs:
* RepeatScout
* [[RepeatScout]]
* RECON
* RECON
* PILER
* PILER
* [[WindowMasker]]
* RAP
* [[orrb]] a very fast denovo repeat finder for alignment only
Some of these programs find repeats on their own, but some create custom libraries for RepeatMasker.
== History ==
RepeatMasker was created a long time ago.  [[Arian Smit]] was the original author but [[Robert Hubley]] is now an author as well.  In 2002, RECON was created by [[Sean Eddy]]'s lab at Wasington Univeristy of St. Louis.  In 2005, RepeatScout and PILER were both made. 
== Comparing Repeat Finders ==
Currently there are published comparisons between RepeatScout and RECON, and also comparisons with RepeatMasker.  Eventually this section will detail some experiments too.
== See Also ==
* [http://www.repeatmasker.org/ RepeatMasker]
[[Category:Browser Development]]

Latest revision as of 20:16, 20 January 2010

A denovo repeat finder is a program designed to find repeats in DNA sequence without using the RepeatMasker library. Currently there are a few choices for denovo repeat programs:

Some of these programs find repeats on their own, but some create custom libraries for RepeatMasker.

History

RepeatMasker was created a long time ago. Arian Smit was the original author but Robert Hubley is now an author as well. In 2002, RECON was created by Sean Eddy's lab at Wasington Univeristy of St. Louis. In 2005, RepeatScout and PILER were both made.

Comparing Repeat Finders

Currently there are published comparisons between RepeatScout and RECON, and also comparisons with RepeatMasker. Eventually this section will detail some experiments too.

See Also