This reports the protocol used to align the Rice_ESTcluster_TIGR features to Maize_BACs_20060126.
Mon Feb 13 13:19:46 2006


Source of Rice_ESTcluster_TIGR : Downloaded from TIGR at ftp://ftp.tigr.org/pub/data/tgi/Oryza_sativa/OGI.release_16.zip 

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

89147 Rice_ESTcluster_TIGR 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 : 11684
# unique Features these alignments represent: 9306
% of total features these alignments represent : 10.44 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 3233
150	 1611
200	 1138
250	 886
300	 794
350	 521
400	 519
450	 388
500	 319
550	 211
600	 205
650	 181
700	 137
750	 164
800	 113
10000	 1264

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 6854
# unique Features these remaining alignments represent: 5477
% of total features these alignments represent : 6.14 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 4864
2	 357
3	 47
4	 42
5	 88
6	 46
8	 33
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 5719
# unique Features these remaining alignments represent: 5268
% of total features these alignments represent : 5.91 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 2
30	 8
40	 63
50	 201
60	 376
70	 490
80	 977
90	 2815
95	 600
100	 187

Following is the distribution of Gaps
Gaps	# features
--------	--------
1000	 4085
2000	 654
3000	 321
4000	 143
5000	 63
6000	 42
7000	 36
8000	 45
9000	 30
10000	 15

Following is the final summary
# alignments : 5719
# unique Features these alignments represent: 5268
% of total features these alignments represent : 5.91 %