This reports the protocol used to align the Millet_EST features to Maize_BACs_20060126.
Mon Feb 13 12:18:00 2006


Source of Millet_EST : Downloaded from genbank with query ' Pennisetum glaucum AND gbdiv_est[PROP]' 

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

2532 Millet_EST 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 : 382
# unique Features these alignments represent: 276
% of total features these alignments represent : 10.90 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 66
150	 45
200	 46
250	 50
300	 37
350	 18
400	 27
450	 30
500	 21
550	 10
600	 21
650	 7
700	 3
750	 1
800	 0
10000	 0

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 273
# unique Features these remaining alignments represent: 189
% of total features these alignments represent : 7.46 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 141
2	 37
3	 1
4	 1
5	 4
6	 4
8	 1
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 218
# unique Features these remaining alignments represent: 179
% of total features these alignments represent : 7.07 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 1
50	 2
60	 1
70	 2
80	 5
90	 60
95	 87
100	 60

Following is the distribution of Gaps
Gaps	# features
--------	--------
1000	 209
2000	 3
3000	 0
4000	 1
5000	 1
6000	 0
7000	 0
8000	 0
9000	 0
10000	 0

Following is the final summary
# alignments : 218
# unique Features these alignments represent: 179
% of total features these alignments represent : 7.07 %