This reports the protocol used to align the Rice_consensus_Affymetrix features to Maize_BACs.
 Kiran Ratnapu 
Tue May 31 16:21:22 2005


Source of Rice_consensus_Affymetrix : Downloaded from Affymetrix website  

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

57194 Rice_consensus_Affymetrix are aligned to Maize_BACs 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 : 1206
# unique Features these alignments represent: 1011
% of total features these alignments represent : 1.77 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 882
150	 89
200	 27
250	 25
300	 19
350	 16
400	 30
450	 8
500	 19
550	 5
600	 5
650	 7
700	 4
750	 15
800	 7
10000	 48

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 237
# unique Features these remaining alignments represent: 182
% of total features these alignments represent : 0.32 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 158
2	 13
3	 2
4	 1
5	 7
6	 0
8	 1
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 190
# unique Features these remaining alignments represent: 173
% of total features these alignments represent : 0.30 %

% 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	 85
100	 105

Following is the distribution of Rice gaps
Rice_Gaps	# features
--------	--------
1000	 167
2000	 9
3000	 5
4000	 3
5000	 1
6000	 0
7000	 1
8000	 0
9000	 0
10000	 0

Following is the final summary
# alignments : 190
# unique Features these alignments represent: 173
% of total features these alignments represent : 0.30 %