This reports the protocol used to align the Rice_Alta_BACend features to Maize_BACs.
 Kiran Ratnapu 
Mon Mar 28 12:28:16 2005


Source of Rice_Alta_BACend : From genbank nucleotide database with keyword 'OA_BBa'

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

20573 Rice_Alta_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 : 2731
# unique Features these alignments represent: 2048
% of total features these alignments represent : 9.95 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 746
150	 397
200	 255
250	 245
300	 183
350	 150
400	 189
450	 136
500	 140
550	 100
600	 77
650	 60
700	 26
750	 15
800	 7
10000	 5

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 2001
# unique Features these remaining alignments represent: 1465
% of total features these alignments represent : 7.12 %

Rice_gap distribution of the remaining features
Rice_gaps	# alignments
--------	--------
1000	 1911
2000	 4
3000	 4
4000	 3
5000	 0
6000	 1
7000	 1
8000	 4
9000	 2
10000	 2
20000	 8

Alignments with gaps on rice > 4000 bp are filtered
# remaining Alignments : 1922
# unique Features these remaining alignments represent: 1416
% of total features these alignments represent : 6.88 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 1110
2	 206
3	 51
4	 24
5	 13
6	 5
8	 5
9	 2
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 1675
# unique Features these remaining alignments represent: 1367
% of total features these alignments represent : 6.64 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 15
40	 30
50	 82
60	 155
70	 270
80	 439
90	 461
100	 223

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 1410
# unique Features these remaining alignments represent: 1135
% of total features these alignments represent : 5.52 %

Following is the final summary
# alignments : 1410
# unique Features these alignments represent: 1135
% of total features these alignments represent : 5.52 %