This reports the protocol used to align the Barley_tug features to Maize_BACs.
 Kiran Ratnapu 
Tue Mar 29 18:36:44 2005


Source of Barley_tug : http://www.plantgdb.org/download//PlantTUGs/HVtug.gz  

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

53405 Barley_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 : 4510
# unique Features these alignments represent: 3394
% of total features these alignments represent : 6.36 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 1192
150	 617
200	 542
250	 414
300	 396
350	 411
400	 341
450	 366
500	 98
550	 77
600	 18
650	 14
700	 19
750	 3
800	 0
10000	 2

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 2712
# unique Features these remaining alignments represent: 1966
% of total features these alignments represent : 3.68 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 1609
2	 230
3	 26
4	 18
5	 27
6	 41
8	 15
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 2147
# unique Features these remaining alignments represent: 1865
% of total features these alignments represent : 3.49 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 1
40	 0
50	 1
60	 11
70	 34
80	 171
90	 923
95	 551
100	 455

Following is the distribution of Rice gaps
Rice_Gaps	# features
--------	--------
1000	 1994
2000	 88
3000	 31
4000	 4
5000	 4
6000	 1
7000	 2
8000	 5
9000	 0
10000	 2

Following is the final summary
# alignments : 2147
# unique Features these alignments represent: 1865
% of total features these alignments represent : 3.49 %