This reports the protocol used to align the Maize_Marker features to tigrv4-genome.
Fri Apr 14 11:53:45 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 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 : 4537
# unique Features these alignments represent: 3819
% of total features these alignments represent : 54.79 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 628
150	 565
200	 649
250	 539
300	 424
350	 375
400	 377
450	 171
500	 118
550	 86
600	 64
650	 34
700	 20
750	 44
800	 27
10000	 415

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 3360
# unique Features these remaining alignments represent: 2768
% of total features these alignments represent : 39.71 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 2296
2	 420
3	 15
4	 15
5	 13
6	 9
8	 0
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 3181
# unique Features these remaining alignments represent: 2731
% of total features these alignments represent : 39.18 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 1
50	 2
60	 2
70	 25
80	 204
90	 2094
95	 650
100	 203

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 2390
2000	 385
3000	 191
4000	 76
5000	 27
6000	 28
7000	 9
8000	 10
9000	 5
10000	 8

Following is the final summary
# alignments : 3181
# unique Features these alignments represent: 2731
% of total features these alignments represent : 39.18 %