This reports the protocol used to align the RiceCoarctata_BACend_OMAP features to Maize_BACs_20060126.
Mon Feb 13 16:52:29 2006


Source of RiceCoarctata_BACend_OMAP : From genbank Nucleotide database with keyword 'OC__Ba'  

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

195285 RiceCoarctata_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 : 20525
# unique Features these alignments represent: 16806
% of total features these alignments represent : 8.61 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 5017
150	 2612
200	 2227
250	 1943
300	 1513
350	 1547
400	 1199
450	 929
500	 855
550	 694
600	 850
650	 420
700	 347
750	 204
800	 105
10000	 63

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 15563
# unique Features these remaining alignments represent: 12488
% of total features these alignments represent : 6.39 %

Gap distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 15174
2000	 34
3000	 11
4000	 8
5000	 1
6000	 8
7000	 16
8000	 9
9000	 5
10000	 11
20000	 49

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 15227
# unique Features these remaining alignments represent: 12233
% of total features these alignments represent : 6.26 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 10320
2	 1378
3	 286
4	 131
5	 43
6	 30
8	 32
9	 7
10	 0
20	 6
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 13934
# unique Features these remaining alignments represent: 11984
% of total features these alignments represent : 6.14 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 1
30	 25
40	 103
50	 310
60	 910
70	 1610
80	 3141
90	 4775
100	 3059

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 12724
# unique Features these remaining alignments represent: 10853
% of total features these alignments represent : 5.56 %

Following is the final summary
# alignments : 12724
# unique Features these alignments represent: 10853
% of total features these alignments represent : 5.56 %