This reports the protocol used to align the Rice_ArrayOligo_Yale58K features to tigrv4-genome.
Fri Jun 30 20:46:45 2006


Source of Rice_ArrayOligo_Yale58K : These are Rice Gene Micro Array Oligos from Tim Nelson's lab at Yale University, this oligo set is derived from a combination of indica and japonica sequence.  

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

58404 Rice_ArrayOligo_Yale58K 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 : 72721
# unique Features these alignments represent: 53906
% of total features these alignments represent : 92.30 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
10	 0
20	 0
30	 25
40	 300

Alignments with matches less than 10 bp are deleted
# remaining Alignments : 72721
# unique Features these remaining alignments represent: 53906
% of total features these alignments represent : 92.30 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 50516
2	 1873
3	 493
4	 219
5	 139
6	 96
8	 148
9	 42
10	 34
20	 179
30	 69
40	 24
50	 19
100	 24

 Features that hit more than thrice are deleted.  
# remaining Alignments : 55741
# unique Features these remaining alignments represent: 52882
% of total features these alignments represent : 90.55 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 0
50	 0
60	 0
70	 1
80	 6
90	 271
95	 2173
100	 53290

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 55554
2000	 105
3000	 24
4000	 10
5000	 5
6000	 5
7000	 4
8000	 3
9000	 1
10000	 1

Following is the final summary
# alignments : 55741
# unique Features these alignments represent: 52882
% of total features these alignments represent : 90.55 %