This reports the protocol used to align the Rice_Glaberrima_BACend features to Maize_BACs.
 Kiran Ratnapu 
Mon Mar 28 12:02:14 2005


Source of Rice_Glaberrima_BACend : From genbank nucleotide database with keyword 'OG_BBa'

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

66804 Rice_Glaberrima_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 : 8726
# unique Features these alignments represent: 6724
% of total features these alignments represent : 10.07 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 2781
150	 1075
200	 754
250	 706
300	 609
350	 500
400	 647
450	 442
500	 328
550	 317
600	 238
650	 123
700	 97
750	 63
800	 36
10000	 10

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 5961
# unique Features these remaining alignments represent: 4499
% of total features these alignments represent : 6.73 %

Rice_gap distribution of the remaining features
Rice_gaps	# alignments
--------	--------
1000	 5763
2000	 5
3000	 1
4000	 0
5000	 0
6000	 3
7000	 4
8000	 5
9000	 1
10000	 4
20000	 20

Alignments with gaps on rice > 4000 bp are filtered
# remaining Alignments : 5769
# unique Features these remaining alignments represent: 4389
% of total features these alignments represent : 6.57 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 3578
2	 571
3	 106
4	 55
5	 30
6	 17
8	 22
9	 6
10	 0
20	 4
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 5038
# unique Features these remaining alignments represent: 4255
% of total features these alignments represent : 6.37 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 1
30	 41
40	 77
50	 239
60	 459
70	 733
80	 734
90	 1111
100	 1643

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 4282
# unique Features these remaining alignments represent: 3604
% of total features these alignments represent : 5.39 %

Following is the final summary
# alignments : 4282
# unique Features these alignments represent: 3604
% of total features these alignments represent : 5.39 %