This reports the protocol used to align the Rice_ArrayConsensus_Affy57K features to Maize_BACs_20060126.
Fri Feb 24 09:57:20 2006


Source of Rice_ArrayConsensus_Affy57K : Downloaded from Affymetrix website  

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

57194 Rice_ArrayConsensus_Affy57K 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 : 7773
# unique Features these alignments represent: 7125
% of total features these alignments represent : 12.46 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 2352
150	 956
200	 746
250	 510
300	 486
350	 339
400	 295
450	 227
500	 175
550	 173
600	 139
650	 136
700	 118
750	 104
800	 104
10000	 913

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 4484
# unique Features these remaining alignments represent: 4215
% of total features these alignments represent : 7.37 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 3993
2	 205
3	 4
4	 2
5	 9
6	 0
8	 2
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 4415
# unique Features these remaining alignments represent: 4202
% of total features these alignments represent : 7.35 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 1
30	 7
40	 17
50	 43
60	 94
70	 229
80	 799
90	 2589
95	 527
100	 109

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 3186
2000	 476
3000	 257
4000	 138
5000	 60
6000	 46
7000	 40
8000	 37
9000	 18
10000	 20

Following is the final summary
# alignments : 4415
# unique Features these alignments represent: 4202
% of total features these alignments represent : 7.35 %