This reports the protocol used to align the Rice_tug features to Maize_BACs.
 Kiran Ratnapu 
Tue Mar 29 19:26:42 2005


Source of Rice_tug : http://www.plantgdb.org/download//PlantTUGs/Oryzasativa.TUG.fasta.gz  

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

100750 Rice_tug 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-Coding' data sets.

Initial summary
# alignments : 6949
# unique Features these alignments represent: 4260
% of total features these alignments represent : 4.23 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 3583
150	 1048
200	 827
250	 522
300	 325
350	 233
400	 166
450	 98
500	 65
550	 48
600	 19
650	 7
700	 4
750	 3
800	 0
10000	 1

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 2333
# unique Features these remaining alignments represent: 1961
% of total features these alignments represent : 1.95 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 1728
2	 179
3	 15
4	 16
5	 12
6	 3
8	 8
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 2131
# unique Features these remaining alignments represent: 1922
% of total features these alignments represent : 1.91 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 3
50	 2
60	 0
70	 35
80	 188
90	 1223
95	 512
100	 168

Following is the distribution of Rice gaps
Rice_Gaps	# features
--------	--------
1000	 1943
2000	 116
3000	 27
4000	 9
5000	 3
6000	 7
7000	 5
8000	 3
9000	 1
10000	 4

Following is the final summary
# alignments : 2131
# unique Features these alignments represent: 1922
% of total features these alignments represent : 1.91 %