This reports the protocol used to align the Millet_EST features to tigrv4-genome.
Fri Apr 14 11:43:50 2006


Source of Millet_EST : from Gramene markers database, originally Downloaded from genbank with query ' Pennisetum glaucum AND gbdiv_est[PROP]' 

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

3519 Millet_EST are aligned to tigrv4-genome 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 : 2513
# unique Features these alignments represent: 1806
% of total features these alignments represent : 51.32 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 290
150	 256
200	 360
250	 213
300	 229
350	 206
400	 203
450	 181
500	 138
550	 102
600	 95
650	 67
700	 61
750	 74
800	 26
10000	 12

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 1970
# unique Features these remaining alignments represent: 1367
% of total features these alignments represent : 38.85 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 1229
2	 30
3	 12
4	 9
5	 14
6	 8
8	 60
9	 5
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 1325
# unique Features these remaining alignments represent: 1271
% of total features these alignments represent : 36.12 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 0
50	 1
60	 2
70	 9
80	 66
90	 789
95	 415
100	 43

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 1122
2000	 142
3000	 25
4000	 12
5000	 1
6000	 2
7000	 7
8000	 0
9000	 1
10000	 0

Following is the final summary
# alignments : 1325
# unique Features these alignments represent: 1271
% of total features these alignments represent : 36.12 %