This reports the protocol used to align the Maize_ESTcluster_MMPconsensus features to Maize_BACs_20060126.
Mon Feb 13 20:14:25 2006


Source of Maize_ESTcluster_MMPconsensus : MaizeDB Unigenes, these are obtained from Mary Polacco ??? 

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

10678 Maize_ESTcluster_MMPconsensus are aligned to Maize_BACs_20060126 using blat with blat parameters -minScore=120 followed by PslReps with -singleHit. This was followed by a filtering procedure described below and applied in general to 'Coding-SameSpecies' data sets.

Initial summary
# alignments : 1582
# unique Features these alignments represent: 1350
% of total features these alignments represent : 12.64 %

The following is the distribution of the feature coverage 
%coverage	no of alignments
--------	--------
9	 32
19	 164
29	 135
39	 124
49	 108
59	 122
69	 159
79	 170
89	 139
90	 20
91	 17
92	 17
93	 16
94	 28
95	 39
96	 43
97	 41
98	 73
99	 70
100	 65

 Alignments less than 95 % coverage are deleted
# remaining Alignments : 292
# unique Features these remaining alignments represent: 268
% of total features these alignments represent : 2.51 %

Gap distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 148
2000	 56
3000	 33
4000	 21
5000	 12
6000	 8
7000	 1
8000	 3
9000	 3
10000	 1
20000	 4

Alignments with gaps  > 4000 bp are deleted
# remaining Alignments : 258
# unique Features these remaining alignments represent: 235
% of total features these alignments represent : 2.20 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 0
92	 0
93	 0
94	 0
95	 0
96	 3
97	 6
98	 26
99	 116
100	 107

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 213
2	 21
3	 1
4	 0
5	 0
6	 0
8	 0
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than four times are deleted.  
# remaining Alignments : 258
# unique Features these remaining alignments represent: 235
% of total features these alignments represent : 2.20 %