This reports the protocol used to align the Rice_Rufipogon_BACend features to Maize_BACs.
 Kiran Ratnapu 
Mon Mar 28 11:54:59 2005


Source of Rice_Rufipogon_BACend : From genbank Nucleotide database with keyword 'OR_CBa'  

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

71006 Rice_Rufipogon_BACend are aligned to Maize_BACs 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 : 12952
# unique Features these alignments represent: 9895
% of total features these alignments represent : 13.94 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 3837
150	 1363
200	 919
250	 956
300	 940
350	 720
400	 950
450	 854
500	 689
550	 492
600	 577
650	 233
700	 144
750	 133
800	 110
10000	 35

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 9140
# unique Features these remaining alignments represent: 6801
% of total features these alignments represent : 9.58 %

Rice_gap distribution of the remaining features
Rice_gaps	# alignments
--------	--------
1000	 8774
2000	 6
3000	 0
4000	 2
5000	 6
6000	 6
7000	 12
8000	 3
9000	 21
10000	 5
20000	 30

Alignments with gaps on rice > 4000 bp are filtered
# remaining Alignments : 8782
# unique Features these remaining alignments represent: 6577
% of total features these alignments represent : 9.26 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 5208
2	 993
3	 174
4	 71
5	 69
6	 31
8	 23
9	 3
10	 4
20	 1
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 7716
# unique Features these remaining alignments represent: 6375
% of total features these alignments represent : 8.98 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 7
30	 34
40	 172
50	 542
60	 940
70	 1295
80	 999
90	 1525
100	 2202

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 6140
# unique Features these remaining alignments represent: 5039
% of total features these alignments represent : 7.10 %

Following is the final summary
# alignments : 6140
# unique Features these alignments represent: 5039
% of total features these alignments represent : 7.10 %