This reports the protocol used to align the Wheat_ArrayConsensus_Affy61K features to tigrv4-genome.
Fri Apr 14 12:02:14 2006


Source of Wheat_ArrayConsensus_Affy61K : Downloaded from Affymetrix website  

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

61115 Wheat_ArrayConsensus_Affy61K are aligned to tigrv4-genome 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 : 32940
# unique Features these alignments represent: 30225
% of total features these alignments represent : 49.46 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 4442
150	 4413
200	 4506
250	 3993
300	 3201
350	 2485
400	 1939
450	 1396
500	 983
550	 815
600	 643
650	 518
700	 554
750	 447
800	 386
10000	 2219

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 24182
# unique Features these remaining alignments represent: 22043
% of total features these alignments represent : 36.07 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 21146
2	 470
3	 107
4	 81
5	 96
6	 92
8	 36
9	 6
10	 5
20	 4
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 22407
# unique Features these remaining alignments represent: 21723
% of total features these alignments represent : 35.54 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 1
30	 0
40	 3
50	 10
60	 34
70	 171
80	 1438
90	 13902
95	 6118
100	 730

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 16183
2000	 3104
3000	 1418
4000	 636
5000	 253
6000	 121
7000	 96
8000	 62
9000	 37
10000	 38

Following is the final summary
# alignments : 22407
# unique Features these alignments represent: 21723
% of total features these alignments represent : 35.54 %