This reports the protocol used to align the Wheat_tug features to Maize_BACs.
 Kiran Ratnapu 
Tue Mar 29 18:48:16 2005


Source of Wheat_tug : http://www.plantgdb.org/download//PlantTUGs/TAtug.gz  

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

107556 Wheat_tug are aligned to Maize_BACs 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 : 8521
# unique Features these alignments represent: 7429
% of total features these alignments represent : 6.91 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 2751
150	 1542
200	 1140
250	 807
300	 623
350	 470
400	 333
450	 284
500	 187
550	 113
600	 66
650	 44
700	 42
750	 27
800	 28
10000	 64

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 4255
# unique Features these remaining alignments represent: 3783
% of total features these alignments represent : 3.52 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 3426
2	 313
3	 23
4	 7
5	 8
6	 1
8	 3
9	 0
10	 0
20	 1
30	 1
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 4121
# unique Features these remaining alignments represent: 3762
% of total features these alignments represent : 3.50 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 1
30	 0
40	 4
50	 15
60	 27
70	 99
80	 404
90	 2118
95	 933
100	 520

Following is the distribution of Rice gaps
Rice_Gaps	# features
--------	--------
1000	 3546
2000	 269
3000	 136
4000	 46
5000	 17
6000	 16
7000	 16
8000	 6
9000	 8
10000	 8

Following is the final summary
# alignments : 4121
# unique Features these alignments represent: 3762
% of total features these alignments represent : 3.50 %