This reports the protocol used to align the RiceIndica_EST_BGI features to Maize_BACs_20060126.
Mon Feb 13 13:33:38 2006


Source of RiceIndica_EST_BGI : Oryza indica ESTs downloaded from http://btn.genomics.org.cn/ 

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

85719 RiceIndica_EST_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 : 9369
# unique Features these alignments represent: 7872
% of total features these alignments represent : 9.18 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 2444
150	 1473
200	 1518
250	 1210
300	 958
350	 683
400	 576
450	 369
500	 115
550	 20
600	 2
650	 1
700	 0
750	 0
800	 0
10000	 0

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 5482
# unique Features these remaining alignments represent: 4510
% of total features these alignments represent : 5.26 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 3870
2	 522
3	 35
4	 18
5	 26
6	 22
8	 17
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 5019
# unique Features these remaining alignments represent: 4427
% of total features these alignments represent : 5.16 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 1
50	 1
60	 15
70	 122
80	 358
90	 2804
95	 1406
100	 312

Following is the distribution of Gaps
Gaps	# features
--------	--------
1000	 4528
2000	 284
3000	 104
4000	 25
5000	 15
6000	 7
7000	 6
8000	 5
9000	 6
10000	 5

Following is the final summary
# alignments : 5019
# unique Features these alignments represent: 4427
% of total features these alignments represent : 5.16 %