From fd2d47f48486c5f74100571c785e047d8312cc05 Mon Sep 17 00:00:00 2001 From: Brandon King Date: Tue, 24 Oct 2006 17:01:13 +0000 Subject: [PATCH] Mussa Manual: spelling, wording, and grammer --- doc/manual/mussagl_manual.rst | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst index 18a8a1a..5e551e7 100644 --- a/doc/manual/mussagl_manual.rst +++ b/doc/manual/mussagl_manual.rst @@ -5,7 +5,7 @@ Mussagl Manual Brandon W. King --------------- -Last updated: Oct 18th, 2006 +Last updated: Oct 20th, 2006 Updated to Mussagl build: (In process to 424) @@ -1271,11 +1271,11 @@ FIXME: Include transitivity info. Repeats ~~~~~~~ -The algorithm Mussa uses to find conserved sequences is sensative to -repeated DNA segments, which are naturally apart of many genomes. The -problem with repeats, is that one repeat from one sequence can show up -many times in another sequence. Every connection Mussa makes takes up -memory, and it also takes time to store and process the results. +The algorithm Mussa uses to find conserved sequences is sensitive to +repeated DNA segments, which are frequently occurring in most +genomes. The problem with repeats, is that one repeat from one +sequence can show up many times in another sequence. Every connection +Mussa makes takes up memory and CPU time to process. The formula for the number of connections, C, that will be made for R instances of a single repeat (meaning R copies of one repeat in each @@ -1317,9 +1317,9 @@ you a C of 2500, ends up with a C^2 of 6,250,000. **Conclusion: repeats cause the processing time of Mussa to skyrocket.** -One, way to deal with a situation where you have lots of repeats in -your sequences is to use shorter sequences lengths and/or repeat mask -at least one of your sequences. +One way to deal with a situation where you have many repeats in your +sequences is do any of the following: user shorter sequence lengths; +repeat mask one or more of your sequences; or increase the threshold. Details ------- -- 2.30.2