This reports the protocol used to align the RiceIndica_ESTcluster_BGI features to Maize_BACs_20060126.
Mon Feb 13 13:20:42 2006


Source of RiceIndica_ESTcluster_BGI : Oryza indica clusters downloaded from http://btn.genomics.org.cn/ 

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

23559 RiceIndica_ESTcluster_BGI are aligned to Maize_BACs_20060126 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 : 2336
# unique Features these alignments represent: 2111
% of total features these alignments represent : 8.96 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 594
150	 387
200	 271
250	 270
300	 222
350	 132
400	 112
450	 60
500	 44
550	 32
600	 33
650	 25
700	 19
750	 18
800	 10
10000	 107

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 1361
# unique Features these remaining alignments represent: 1234
% of total features these alignments represent : 5.24 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 1142
2	 77
3	 8
4	 1
5	 2
6	 2
8	 2
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 1320
# unique Features these remaining alignments represent: 1227
% of total features these alignments represent : 5.21 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 1
50	 3
60	 3
70	 30
80	 141
90	 884
95	 228
100	 30

Following is the distribution of Gaps
Gaps	# features
--------	--------
1000	 1048
2000	 133
3000	 53
4000	 24
5000	 14
6000	 9
7000	 6
8000	 9
9000	 5
10000	 2

Following is the final summary
# alignments : 1320
# unique Features these alignments represent: 1227
% of total features these alignments represent : 5.21 %