This reports the protocol used to align the Wheat_ArrayConsensus_Affy61K features to Maize_BACs_20060126.
Fri Feb 24 09:57:27 2006


Source of Wheat_ArrayConsensus_Affy61K : Downloaded from Affymetrix website  

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

61115 Wheat_ArrayConsensus_Affy61K 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 : 6511
# unique Features these alignments represent: 5049
% of total features these alignments represent : 8.26 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 1645
150	 991
200	 842
250	 669
300	 510
350	 426
400	 403
450	 293
500	 169
550	 152
600	 78
650	 53
700	 39
750	 30
800	 33
10000	 178

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 3887
# unique Features these remaining alignments represent: 2953
% of total features these alignments represent : 4.83 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 2537
2	 239
3	 41
4	 25
5	 53
6	 45
8	 12
9	 0
10	 0
20	 0
30	 1
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 3138
# unique Features these remaining alignments represent: 2817
% of total features these alignments represent : 4.61 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 4
50	 6
60	 31
70	 73
80	 264
90	 1538
95	 710
100	 512

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 2603
2000	 279
3000	 97
4000	 63
5000	 16
6000	 14
7000	 12
8000	 8
9000	 10
10000	 3

Following is the final summary
# alignments : 3138
# unique Features these alignments represent: 2817
% of total features these alignments represent : 4.61 %