This reports the protocol used to align the Barley_ArrayExemplar_Affy22K features to Maize_BACs_20060126.
Fri Feb 24 09:57:09 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 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 : 2414
# unique Features these alignments represent: 2152
% of total features these alignments represent : 10.13 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 553
150	 336
200	 281
250	 240
300	 172
350	 169
400	 121
450	 84
500	 69
550	 62
600	 58
650	 34
700	 45
750	 27
800	 17
10000	 146

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 1532
# unique Features these remaining alignments represent: 1356
% of total features these alignments represent : 6.38 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 1231
2	 109
3	 4
4	 2
5	 4
6	 1
8	 5
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 1461
# unique Features these remaining alignments represent: 1344
% of total features these alignments represent : 6.33 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 1
40	 0
50	 1
60	 14
70	 44
80	 242
90	 925
95	 203
100	 31

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 1120
2000	 151
3000	 86
4000	 33
5000	 17
6000	 10
7000	 3
8000	 5
9000	 8
10000	 7

Following is the final summary
# alignments : 1461
# unique Features these alignments represent: 1344
% of total features these alignments represent : 6.33 %