This reports the protocol used to align the RicePunctata_BACend_OMAP features to Maize_BACs_20060126.
Mon Feb 13 17:52:06 2006


Source of RicePunctata_BACend_OMAP : Downloaded from genbank nucleotide databse with keyword 'OP__Ba'   

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

68384 RicePunctata_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 : 10816
# unique Features these alignments represent: 8053
% of total features these alignments represent : 11.78 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 3380
150	 1494
200	 1052
250	 980
300	 743
350	 571
400	 540
450	 426
500	 456
550	 413
600	 342
650	 159
700	 98
750	 79
800	 58
10000	 25

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 7457
# unique Features these remaining alignments represent: 5585
% of total features these alignments represent : 8.17 %

Gap distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 7069
2000	 15
3000	 13
4000	 9
5000	 2
6000	 10
7000	 9
8000	 14
9000	 7
10000	 16
20000	 76

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 7106
# unique Features these remaining alignments represent: 5364
% of total features these alignments represent : 7.84 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 4385
2	 643
3	 179
4	 66
5	 28
6	 26
8	 13
9	 17
10	 2
20	 5
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 6208
# unique Features these remaining alignments represent: 5207
% of total features these alignments represent : 7.61 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 3
30	 26
40	 125
50	 361
60	 656
70	 966
80	 1388
90	 1641
100	 1042

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 5126
# unique Features these remaining alignments represent: 4251
% of total features these alignments represent : 6.22 %

Following is the final summary
# alignments : 5126
# unique Features these alignments represent: 4251
% of total features these alignments represent : 6.22 %