This reports the protocol used to align the Rice_unmapped_BAC_back features to Maize_BACs_20060126.
Mon Feb 13 19:12:32 2006


Source of Rice_unmapped_BAC_back : Downloaded from NCBI Genbank 

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

682 Rice_unmapped_BAC_back 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 : 141
# unique Features these alignments represent: 120
% of total features these alignments represent : 17.60 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 51
150	 20
200	 9
250	 11
300	 3
350	 7
400	 6
450	 3
500	 4
550	 3
600	 0
650	 1
700	 0
750	 3
800	 0
10000	 20

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 91
# unique Features these remaining alignments represent: 74
% of total features these alignments represent : 10.85 %

Gap distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 85
2000	 1
3000	 1
4000	 0
5000	 0
6000	 0
7000	 0
8000	 0
9000	 0
10000	 0
20000	 1

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 87
# unique Features these remaining alignments represent: 71
% of total features these alignments represent : 10.41 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 63
2	 6
3	 0
4	 1
5	 0
6	 0
8	 1
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 75
# unique Features these remaining alignments represent: 69
% of total features these alignments represent : 10.12 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 1
40	 0
50	 5
60	 7
70	 7
80	 19
90	 26
100	 10

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 64
# unique Features these remaining alignments represent: 58
% of total features these alignments represent : 8.50 %

Following is the final summary
# alignments : 64
# unique Features these alignments represent: 58
% of total features these alignments represent : 8.50 %