This reports the protocol used to align the Rice_Nivara_BACend features to Maize_BACs.
 Kiran Ratnapu 
Mon Mar 28 11:59:02 2005


Source of Rice_Nivara_BACend : From genbank Nucleotide database with keyword 'OR_BBa'  

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

106130 Rice_Nivara_BACend 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-Genomic' data sets.

Initial summary
# alignments : 20142
# unique Features these alignments represent: 15221
% of total features these alignments represent : 14.34 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 5463
150	 2206
200	 1634
250	 1487
300	 1530
350	 1274
400	 1555
450	 1493
500	 1122
550	 750
600	 672
650	 302
700	 247
750	 200
800	 142
10000	 65

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 14726
# unique Features these remaining alignments represent: 10858
% of total features these alignments represent : 10.23 %

Rice_gap distribution of the remaining features
Rice_gaps	# alignments
--------	--------
1000	 14248
2000	 10
3000	 0
4000	 7
5000	 2
6000	 4
7000	 22
8000	 8
9000	 31
10000	 6
20000	 50

Alignments with gaps on rice > 4000 bp are filtered
# remaining Alignments : 14265
# unique Features these remaining alignments represent: 10553
% of total features these alignments represent : 9.94 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 8218
2	 1684
3	 313
4	 157
5	 82
6	 43
8	 45
9	 5
10	 5
20	 1
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 12525
# unique Features these remaining alignments represent: 10215
% of total features these alignments represent : 9.62 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 4
30	 58
40	 224
50	 949
60	 1479
70	 2125
80	 1786
90	 2306
100	 3594

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 9991
# unique Features these remaining alignments represent: 8061
% of total features these alignments represent : 7.60 %

Following is the final summary
# alignments : 9991
# unique Features these alignments represent: 8061
% of total features these alignments represent : 7.60 %