This reports the protocol used to align the Rice_Australiensis_BACend features to Maize_BACs.
 Kiran Ratnapu 
Mon Mar 28 12:36:37 2005


Source of Rice_Australiensis_BACend : From genbank nucleotide database with keyword 'OA_ABa'

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

137530 Rice_Australiensis_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 : 39834
# unique Features these alignments represent: 26786
% of total features these alignments represent : 19.48 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 11200
150	 4144
200	 3614
250	 3189
300	 2357
350	 3073
400	 3212
450	 2671
500	 2542
550	 1404
600	 959
650	 553
700	 372
750	 312
800	 176
10000	 56

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 28726
# unique Features these remaining alignments represent: 19058
% of total features these alignments represent : 13.86 %

Rice_gap distribution of the remaining features
Rice_gaps	# alignments
--------	--------
1000	 28044
2000	 31
3000	 12
4000	 13
5000	 5
6000	 10
7000	 43
8000	 30
9000	 25
10000	 13
20000	 64

Alignments with gaps on rice > 4000 bp are filtered
# remaining Alignments : 28100
# unique Features these remaining alignments represent: 18642
% of total features these alignments represent : 13.55 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 13679
2	 2993
3	 947
4	 461
5	 207
6	 137
8	 156
9	 15
10	 12
20	 35
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 22506
# unique Features these remaining alignments represent: 17619
% of total features these alignments represent : 12.81 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 14
30	 235
40	 594
50	 1931
60	 3484
70	 3924
80	 5991
90	 3723
100	 2610

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 16568
# unique Features these remaining alignments represent: 12689
% of total features these alignments represent : 9.23 %

Following is the final summary
# alignments : 16568
# unique Features these alignments represent: 12689
% of total features these alignments represent : 9.23 %