This reports the protocol used to align the RiceGlaberrima_BACend_OMAP features to Maize_BACs_20060126.
Mon Feb 13 23:46:44 2006


Source of RiceGlaberrima_BACend_OMAP : Downloaded from genbank nucleotide databse with keyword 'OG_BBa'   

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

66821 RiceGlaberrima_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 : 8868
# unique Features these alignments represent: 6848
% of total features these alignments represent : 10.25 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 2771
150	 1113
200	 793
250	 741
300	 587
350	 508
400	 645
450	 465
500	 345
550	 336
600	 234
650	 124
700	 97
750	 63
800	 36
10000	 10

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 6121
# unique Features these remaining alignments represent: 4583
% of total features these alignments represent : 6.86 %

Gap distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 5924
2000	 3
3000	 4
4000	 0
5000	 1
6000	 3
7000	 3
8000	 5
9000	 5
10000	 3
20000	 17

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 5931
# unique Features these remaining alignments represent: 4486
% of total features these alignments represent : 6.71 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 3668
2	 555
3	 124
4	 57
5	 27
6	 15
8	 24
9	 12
10	 2
20	 2
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 5150
# unique Features these remaining alignments represent: 4347
% of total features these alignments represent : 6.51 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 37
40	 82
50	 206
60	 436
70	 776
80	 804
90	 1150
100	 1659

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 4450
# unique Features these remaining alignments represent: 3744
% of total features these alignments represent : 5.60 %

Following is the final summary
# alignments : 4450
# unique Features these alignments represent: 3744
% of total features these alignments represent : 5.60 %