This reports the protocol used to align the RiceRufipogon_BACend_OMAP features to Maize_BACs_20060126.
Mon Feb 13 18:19:59 2006


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

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

70982 RiceRufipogon_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 : 13018
# unique Features these alignments represent: 10093
% of total features these alignments represent : 14.22 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 3842
150	 1378
200	 941
250	 965
300	 967
350	 689
400	 962
450	 921
500	 652
550	 484
600	 579
650	 223
700	 138
750	 132
800	 110
10000	 35

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 9198
# unique Features these remaining alignments represent: 6946
% of total features these alignments represent : 9.79 %

Gap distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 8852
2000	 4
3000	 1
4000	 2
5000	 5
6000	 6
7000	 12
8000	 5
9000	 13
10000	 5
20000	 37

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 8859
# unique Features these remaining alignments represent: 6722
% of total features these alignments represent : 9.47 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 5437
2	 897
3	 183
4	 84
5	 61
6	 28
8	 20
9	 5
10	 6
20	 1
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 7780
# unique Features these remaining alignments represent: 6517
% of total features these alignments represent : 9.18 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 3
30	 46
40	 185
50	 565
60	 916
70	 1308
80	 996
90	 1564
100	 2197

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 6186
# unique Features these remaining alignments represent: 5151
% of total features these alignments represent : 7.26 %

Following is the final summary
# alignments : 6186
# unique Features these alignments represent: 5151
% of total features these alignments represent : 7.26 %