This reports the protocol used to align the RiceBrachyantha_BACend_OMAP features to Maize_BACs_20060126.
Mon Feb 13 16:58:18 2006


Source of RiceBrachyantha_BACend_OMAP : Downloaded from Genbank with 'Brachyantha' as keyword  

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

67364 RiceBrachyantha_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 : 7962
# unique Features these alignments represent: 6377
% of total features these alignments represent : 9.47 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 2601
150	 979
200	 747
250	 589
300	 474
350	 484
400	 504
450	 344
500	 373
550	 302
600	 249
650	 120
700	 99
750	 69
800	 22
10000	 6

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 5407
# unique Features these remaining alignments represent: 4289
% of total features these alignments represent : 6.37 %

Gap distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 4970
2000	 8
3000	 3
4000	 1
5000	 5
6000	 5
7000	 8
8000	 8
9000	 9
10000	 8
20000	 55

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 4982
# unique Features these remaining alignments represent: 4059
% of total features these alignments represent : 6.03 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 3411
2	 511
3	 74
4	 31
5	 14
6	 5
8	 9
9	 2
10	 2
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 4655
# unique Features these remaining alignments represent: 3996
% of total features these alignments represent : 5.93 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 8
40	 47
50	 111
60	 253
70	 682
80	 890
90	 1326
100	 1338

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 4260
# unique Features these remaining alignments represent: 3664
% of total features these alignments represent : 5.44 %

Following is the final summary
# alignments : 4260
# unique Features these alignments represent: 3664
% of total features these alignments represent : 5.44 %