This reports the protocol used to align the Sorghum_tug features to Maize_BACs.
 Kiran Ratnapu 
Tue Mar 29 18:57:06 2005


Source of Sorghum_tug : http://www.plantgdb.org/download//PlantTUGs/SBtug.gz  

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

25190 Sorghum_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 : 2528
# unique Features these alignments represent: 1566
% of total features these alignments represent : 6.22 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 512
150	 298
200	 277
250	 233
300	 275
350	 261
400	 217
450	 172
500	 155
550	 71
600	 42
650	 12
700	 1
750	 0
800	 0
10000	 2

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 1724
# unique Features these remaining alignments represent: 1057
% of total features these alignments represent : 4.20 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 810
2	 121
3	 13
4	 18
5	 44
6	 29
8	 22
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 1091
# unique Features these remaining alignments represent: 944
% of total features these alignments represent : 3.75 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 1
50	 1
60	 3
70	 15
80	 45
90	 227
95	 626
100	 173

Following is the distribution of Rice gaps
Rice_Gaps	# features
--------	--------
1000	 956
2000	 73
3000	 25
4000	 12
5000	 6
6000	 5
7000	 4
8000	 1
9000	 0
10000	 3

Following is the final summary
# alignments : 1091
# unique Features these alignments represent: 944
% of total features these alignments represent : 3.75 %