This reports the protocol used to align the RiceNivara_BACend_OMAP features to Maize_BACs_20060126.
Mon Feb 13 17:52:08 2006


Source of RiceNivara_BACend_OMAP : From genbank Nucleotide database with keyword 'OR_BBa'  

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

106124 RiceNivara_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 : 20181
# unique Features these alignments represent: 15403
% of total features these alignments represent : 14.51 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 5485
150	 2076
200	 1638
250	 1499
300	 1611
350	 1251
400	 1587
450	 1566
500	 1110
550	 739
600	 669
650	 296
700	 247
750	 200
800	 142
10000	 65

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 14755
# unique Features these remaining alignments represent: 10974
% of total features these alignments represent : 10.34 %

Gap distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 14263
2000	 7
3000	 3
4000	 8
5000	 1
6000	 5
7000	 15
8000	 15
9000	 14
10000	 15
20000	 47

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 14281
# unique Features these remaining alignments represent: 10674
% of total features these alignments represent : 10.06 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 8471
2	 1552
3	 314
4	 146
5	 92
6	 38
8	 44
9	 8
10	 8
20	 1
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 12517
# unique Features these remaining alignments represent: 10337
% of total features these alignments represent : 9.74 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 3
30	 44
40	 275
50	 887
60	 1462
70	 2212
80	 1671
90	 2357
100	 3606

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 10022
# unique Features these remaining alignments represent: 8207
% of total features these alignments represent : 7.73 %

Following is the final summary
# alignments : 10022
# unique Features these alignments represent: 8207
% of total features these alignments represent : 7.73 %