This reports the protocol used to align the Barley1_GeneChip_exemplars features to Maize_BACs.
 Kiran Ratnapu 
Tue Mar 29 18:38:16 2005


Source of Barley1_GeneChip_exemplars : Obtained from Roger Wise and Stacy Turner   
Publication

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

21239 Barley1_GeneChip_exemplars 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 : 2370
# unique Features these alignments represent: 2087
% of total features these alignments represent : 9.83 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 550
150	 321
200	 287
250	 238
300	 167
350	 163
400	 109
450	 83
500	 83
550	 54
600	 53
650	 33
700	 38
750	 26
800	 22
10000	 143

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 1504
# unique Features these remaining alignments represent: 1318
% of total features these alignments represent : 6.21 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 1185
2	 115
3	 6
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 : 1433
# unique Features these remaining alignments represent: 1306
% of total features these alignments represent : 6.15 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 2
50	 0
60	 12
70	 40
80	 240
90	 906
95	 202
100	 31

Following is the distribution of Rice gaps
Rice_Gaps	# features
--------	--------
1000	 1089
2000	 147
3000	 87
4000	 31
5000	 17
6000	 12
7000	 5
8000	 7
9000	 6
10000	 8

Following is the final summary
# alignments : 1433
# unique Features these alignments represent: 1306
% of total features these alignments represent : 6.15 %