This reports the protocol used to align the Sorghum_ESTcluster3_Pratt features to Maize_BACs_20060126.
Mon Feb 13 15:00:48 2006


Source of Sorghum_ESTcluster3_Pratt : NULL 

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

27436 Sorghum_ESTcluster3_Pratt are aligned to Maize_BACs_20060126 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 : 4354
# unique Features these alignments represent: 3494
% of total features these alignments represent : 12.74 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 851
150	 477
200	 401
250	 317
300	 336
350	 338
400	 313
450	 287
500	 233
550	 215
600	 192
650	 138
700	 105
750	 66
800	 59
10000	 26

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 3034
# unique Features these remaining alignments represent: 2435
% of total features these alignments represent : 8.88 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 2135
2	 215
3	 18
4	 12
5	 7
6	 22
8	 26
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 2619
# unique Features these remaining alignments represent: 2368
% of total features these alignments represent : 8.63 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 1
50	 0
60	 10
70	 20
80	 114
90	 628
95	 1579
100	 267

Following is the distribution of Gaps
Gaps	# features
--------	--------
1000	 2225
2000	 216
3000	 74
4000	 27
5000	 18
6000	 12
7000	 9
8000	 4
9000	 6
10000	 5

Following is the final summary
# alignments : 2619
# unique Features these alignments represent: 2368
% of total features these alignments represent : 8.63 %