This reports the protocol used to align the Maize_ArrayConsensus_Affy18K features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 17:07:06 2007


Source of Maize_ArrayConsensus_Affy18K : Downloaded from Affymetrix website  

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

17555 Maize_ArrayConsensus_Affy18K are aligned to Oryza_sativa_indica-chromosome-20070724 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 : 1441
# unique Features these alignments represent: 1224
% of total features these alignments represent : 6.97 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 674
150	 149
200	 115
250	 97
300	 83
350	 53
400	 89
450	 53
500	 24
550	 18
600	 7
650	 8
700	 12
750	 8
800	 4
10000	 47

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 619
# unique Features these remaining alignments represent: 524
% of total features these alignments represent : 2.98 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 464
2	 39
3	 10
4	 8
5	 3
6	 0
8	 0
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 572
# unique Features these remaining alignments represent: 513
% of total features these alignments represent : 2.92 %

% 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	 415
100	 157

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 425
2000	 85
3000	 20
4000	 4
5000	 6
6000	 6
7000	 2
8000	 4
9000	 2
10000	 0

Following is the final summary
# alignments : 572
# unique Features these alignments represent: 513
% of total features these alignments represent : 2.92 %
  

Last modified: Thu Sep 13 15:01:03 2007