This reports the protocol used to align the Wheat_consensus_Affymetrix features to Maize_BACs.
 Kiran Ratnapu 
Tue May 31 16:23:15 2005


Source of Wheat_consensus_Affymetrix : Downloaded from Affymetrix website  

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

61115 Wheat_consensus_Affymetrix 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 : 2161
# unique Features these alignments represent: 1205
% of total features these alignments represent : 1.97 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 637
150	 208
200	 162
250	 216
300	 166
350	 185
400	 196
450	 175
500	 82
550	 73
600	 9
650	 8
700	 8
750	 4
800	 4
10000	 28

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 1320
# unique Features these remaining alignments represent: 633
% of total features these alignments represent : 1.04 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 410
2	 75
3	 26
4	 20
5	 46
6	 44
8	 11
9	 0
10	 0
20	 0
30	 1
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 638
# unique Features these remaining alignments represent: 511
% of total features these alignments represent : 0.84 %

% 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	 158
100	 480

Following is the distribution of Rice gaps
Rice_Gaps	# features
--------	--------
1000	 550
2000	 53
3000	 17
4000	 5
5000	 2
6000	 0
7000	 1
8000	 3
9000	 3
10000	 0

Following is the final summary
# alignments : 638
# unique Features these alignments represent: 511
% of total features these alignments represent : 0.84 %