This reports the protocol used to align the RiceAustraliensis_BACend_OMAP features to Maize_BACs_20060126.
Mon Feb 13 16:44:55 2006


Source of RiceAustraliensis_BACend_OMAP : Downloaded from genbank nucleotide databse with keyword 'OA_ABa'   

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

128599 RiceAustraliensis_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 : 37514
# unique Features these alignments represent: 25319
% of total features these alignments represent : 19.69 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 10260
150	 3917
200	 3530
250	 2997
300	 2286
350	 2962
400	 3034
450	 2494
500	 2423
550	 1305
600	 927
650	 503
700	 358
750	 298
800	 166
10000	 54

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 27325
# unique Features these remaining alignments represent: 18113
% of total features these alignments represent : 14.08 %

Gap distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 26695
2000	 24
3000	 12
4000	 9
5000	 5
6000	 15
7000	 41
8000	 40
9000	 10
10000	 12
20000	 57

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 26740
# unique Features these remaining alignments represent: 17726
% of total features these alignments represent : 13.78 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 13109
2	 2639
3	 969
4	 483
5	 202
6	 119
8	 144
9	 22
10	 6
20	 32
30	 1
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 21294
# unique Features these remaining alignments represent: 16717
% of total features these alignments represent : 13.00 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 14
30	 168
40	 615
50	 1820
60	 3245
70	 3669
80	 5660
90	 3621
100	 2482

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 15763
# unique Features these remaining alignments represent: 12076
% of total features these alignments represent : 9.39 %

Following is the final summary
# alignments : 15763
# unique Features these alignments represent: 12076
% of total features these alignments represent : 9.39 %