This reports the protocol used to align the Maize_ESTcluster_MMPconsensus features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 15:42:46 2007


Source of Maize_ESTcluster_MMPconsensus : MaizeDB Unigenes, these are obtained from Mary Polacco ??? 

Alignment procedure details 
--------------------------- 

10678 Maize_ESTcluster_MMPconsensus are aligned to Oryza_sativa_indica-chromosome-20070724 using blat with blat parameters -minIdentity=50 followed by PslReps with -singleHit. This was followed by a filtering procedure described below and applied in general to 'CrossSpecies-Coding' data sets.

Initial summary
# alignments : 572
# unique Features these alignments represent: 523
% of total features these alignments represent : 4.90 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 340
150	 70
200	 50
250	 32
300	 20
350	 10
400	 13
450	 10
500	 9
550	 4
600	 3
650	 1
700	 3
750	 4
800	 1
10000	 2

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 165
# unique Features these remaining alignments represent: 154
% of total features these alignments represent : 1.44 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 144
2	 9
3	 1
4	 0
5	 0
6	 0
8	 0
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 165
# unique Features these remaining alignments represent: 154
% of total features these alignments represent : 1.44 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 0
50	 0
60	 0
70	 0
80	 0
90	 0
95	 143
100	 22

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 119
2000	 28
3000	 5
4000	 1
5000	 4
6000	 1
7000	 0
8000	 0
9000	 1
10000	 0

Following is the final summary
# alignments : 165
# unique Features these alignments represent: 154
% of total features these alignments represent : 1.44 %
  

Last modified: Thu Sep 13 15:01:03 2007