This reports the protocol used to align the Barley_ArrayExemplar_Affy22K features to tigrv4-genome.
Fri Apr 14 11:44:00 2006


Source of Barley_ArrayExemplar_Affy22K : Barley GeneChip exemplars were obtained from Roger Wise and Stacy Turner.\nThey are described in \nthis publication. 

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

21239 Barley_ArrayExemplar_Affy22K 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 : 14167
# unique Features these alignments represent: 13372
% of total features these alignments represent : 62.96 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 1237
150	 1116
200	 1293
250	 1236
300	 1217
350	 995
400	 923
450	 800
500	 668
550	 556
600	 549
650	 440
700	 397
750	 348
800	 291
10000	 2101

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 11838
# unique Features these remaining alignments represent: 11190
% of total features these alignments represent : 52.69 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 10891
2	 178
3	 46
4	 22
5	 13
6	 10
8	 20
9	 10
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 11385
# unique Features these remaining alignments represent: 11115
% of total features these alignments represent : 52.33 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 2
50	 7
60	 15
70	 98
80	 993
90	 8248
95	 1898
100	 124

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 6967
2000	 2108
3000	 1100
4000	 470
5000	 207
6000	 104
7000	 65
8000	 43
9000	 34
10000	 14

Following is the final summary
# alignments : 11385
# unique Features these alignments represent: 11115
% of total features these alignments represent : 52.33 %