This reports the protocol used to align the Rice_Japonica_BACend features to Maize_BACs.
 Kiran Ratnapu 
Mon Mar 28 12:21:47 2005


Source of Rice_Japonica_BACend : Downloaded from genbank using the query '(CUGI Rice BAC end) AND (oryza [ORGN])' and only high quality sequence is extracted based on the information from genbank records  

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

88427 Rice_Japonica_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 : 39810
# unique Features these alignments represent: 18102
% of total features these alignments represent : 20.47 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 28133
150	 1355
200	 1292
250	 1609
300	 1466
350	 1651
400	 1339
450	 810
500	 925
550	 184
600	 228
650	 252
700	 242
750	 90
800	 6
10000	 226

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 11699
# unique Features these remaining alignments represent: 7004
% of total features these alignments represent : 7.92 %

Rice_gap distribution of the remaining features
Rice_gaps	# alignments
--------	--------
1000	 10906
2000	 43
3000	 15
4000	 5
5000	 1
6000	 4
7000	 12
8000	 16
9000	 9
10000	 11
20000	 37

Alignments with gaps on rice > 4000 bp are filtered
# remaining Alignments : 10969
# unique Features these remaining alignments represent: 6379
% of total features these alignments represent : 7.21 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 4889
2	 736
3	 148
4	 62
5	 29
6	 127
8	 381
9	 3
10	 1
20	 3
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 6805
# unique Features these remaining alignments represent: 5773
% of total features these alignments represent : 6.53 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 2
30	 20
40	 90
50	 249
60	 481
70	 848
80	 986
90	 1607
100	 2522

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 6029
# unique Features these remaining alignments represent: 5116
% of total features these alignments represent : 5.79 %

Following is the final summary
# alignments : 6029
# unique Features these alignments represent: 5116
% of total features these alignments represent : 5.79 %