This reports the protocol used to align the Rice_unmapped_BAC_front features to Maize_BACs_20060126.
Mon Feb 13 19:17:16 2006


Source of Rice_unmapped_BAC_front : Downloaded from NCBI Genbank 

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

682 Rice_unmapped_BAC_front 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 : 203
# unique Features these alignments represent: 154
% of total features these alignments represent : 22.58 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 86
150	 24
200	 18
250	 15
300	 6
350	 6
400	 3
450	 1
500	 10
550	 5
600	 2
650	 2
700	 5
750	 1
800	 0
10000	 19

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 117
# unique Features these remaining alignments represent: 89
% of total features these alignments represent : 13.05 %

Gap distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 99
2000	 6
3000	 0
4000	 1
5000	 0
6000	 0
7000	 0
8000	 0
9000	 1
10000	 0
20000	 2

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 106
# unique Features these remaining alignments represent: 80
% of total features these alignments represent : 11.73 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 68
2	 8
3	 1
4	 1
5	 0
6	 0
8	 2
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 87
# unique Features these remaining alignments represent: 77
% of total features these alignments represent : 11.29 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 0
40	 1
50	 4
60	 8
70	 13
80	 13
90	 32
100	 16

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 74
# unique Features these remaining alignments represent: 65
% of total features these alignments represent : 9.53 %

Following is the final summary
# alignments : 74
# unique Features these alignments represent: 65
% of total features these alignments represent : 9.53 %