Description of BAG clustering, interpreting results, etc


Steps involved in clustering sequences using BAG:



BAG's xyz.cluster.result file - Interpreting it

Interpreting the clustering result file that BAG produces is quite simple. Here's a sample of what might appear in the xyz.cluster.result file.


CLUSTER 0 size= 10
	gi|21404504|gb|AY085794.1|
	gi|26020031|gb|CA781986.1|CA781986
	gi|26450575|dbj|AK117752.1|
	gi|30690556|ref|NM_179393.1|
	gi|30690561|ref|NM_179394.1|
	gi|19877773|gb|AU238604.1|AU238604
	gi|19875756|gb|AU236587.1|AU236587
	gi|8721421|gb|AV550008.1|AV550008
	gi|8704222|gb|AV542462.1|AV542462
	gi|21403960|gb|AY085250.1|
ENDCLUSTER

 . . .

CLUSTER 102 size= 5 SPLIT INTO  3360 3361
	gi|2413817|gb|AA040993.1|AA040993
	gi|30696476|ref|NM_104768.2|
	gi|23397328|gb|BT000469.2| arti 
	gi|2445950|gb|AA605422.1|AA605422
	gi|21403985|gb|AY085275.1|
ENDCLUSTER
 . . .

In the above result snippet shown:

Other output files produced by BAG:

BAG produces a whole bunch of other files along with the clustering result file. These include xyz.cluster.{cu, history, linear, merge, multidomain, range}. Explaining these result files in detail is not what this document is intended for. Anyway, here's basic information about some of those files:


Arvind Gopu (agopu [at] cs [dot] indiana [dot] edu)
Last Modified: Sat Apr 10 12:24:07 EST 2004