This reports the protocol used to align the Maize_Marker features to Maize_BACs_20060126.
Mon Feb 13 21:39:24 2006


Source of Maize_Marker : From the link http://www.agron.missouri.edu/files_dl/SequenceMap/SequenceMap20030425.txt, unique genbank accessions were pulled out and sequences were extracted from batch entrez 

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

6970 Maize_Marker 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 : 1409
# unique Features these alignments represent: 989
% of total features these alignments represent : 14.19 %

The following is the distribution of the feature coverage 
%coverage	no of alignments
--------	--------
9	 81
19	 82
29	 57
39	 55
49	 39
59	 33
69	 43
79	 50
89	 155
90	 17
91	 18
92	 38
93	 42
94	 48
95	 38
96	 68
97	 66
98	 106
99	 130
100	 243

 Alignments less than 95 % coverage are deleted
# remaining Alignments : 614
# unique Features these remaining alignments represent: 433
% of total features these alignments represent : 6.21 %

Gap distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 492
2000	 69
3000	 28
4000	 10
5000	 3
6000	 1
7000	 0
8000	 3
9000	 1
10000	 2
20000	 3

Alignments with gaps  > 4000 bp are deleted
# remaining Alignments : 599
# unique Features these remaining alignments represent: 421
% of total features these alignments represent : 6.04 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 0
92	 0
93	 0
94	 2
95	 9
96	 18
97	 37
98	 91
99	 285
100	 157

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 291
2	 97
3	 26
4	 2
5	 2
6	 3
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 : 571
# unique Features these remaining alignments represent: 416
% of total features these alignments represent : 5.97 %