This reports the protocol used to align the RiceMinuta_BACend_OMAP features to Maize_BACs_20060126.
Mon Feb 13 17:45:20 2006


Source of RiceMinuta_BACend_OMAP : From genbank Nucleotide database with keyword 'OM__Ba'  

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

169651 RiceMinuta_BACend_OMAP are aligned to Maize_BACs_20060126 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 : 25072
# unique Features these alignments represent: 18400
% of total features these alignments represent : 10.85 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 7721
150	 3510
200	 2643
250	 2532
300	 1658
350	 1685
400	 1391
450	 1465
500	 1047
550	 721
600	 421
650	 149
700	 82
750	 25
800	 20
10000	 2

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 17429
# unique Features these remaining alignments represent: 12208
% of total features these alignments represent : 7.20 %

Gap distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 16803
2000	 18
3000	 9
4000	 3
5000	 3
6000	 25
7000	 17
8000	 67
9000	 32
10000	 22
20000	 72

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 16833
# unique Features these remaining alignments represent: 11866
% of total features these alignments represent : 6.99 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 9187
2	 1649
3	 493
4	 263
5	 128
6	 36
8	 64
9	 30
10	 3
20	 12
30	 1
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 13964
# unique Features these remaining alignments represent: 11329
% of total features these alignments represent : 6.68 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 4
30	 95
40	 250
50	 955
60	 1571
70	 2426
80	 3375
90	 3822
100	 1466

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 11297
# unique Features these remaining alignments represent: 8947
% of total features these alignments represent : 5.27 %

Following is the final summary
# alignments : 11297
# unique Features these alignments represent: 8947
% of total features these alignments represent : 5.27 %