Mussa Manual: spelling, wording, and grammer

diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index 18a8a1ab7fbea8080e588efb0bf63a95820c13e6..5e551e72f37260e67f29c15aee89cf32b9a67bd3 100644 (file)
--- 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
 -------