This reports the protocol used to align the Maize_ArrayGene_NSF58K features to tigrv4-genome.
Fri Apr 14 12:00:05 2006


Source of Maize_ArrayGene_NSF58K : Downloaded from TIGR http://www.maizearray.org/files/remapping_version3_57452_fasta.zip 

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

57452 Maize_ArrayGene_NSF58K 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 : 38853
# unique Features these alignments represent: 36465
% of total features these alignments represent : 63.47 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 4408
150	 3722
200	 3919
250	 3674
300	 3311
350	 2854
400	 2670
450	 2035
500	 1717
550	 1392
600	 1091
650	 926
700	 878
750	 766
800	 700
10000	 4790

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 30783
# unique Features these remaining alignments represent: 29132
% of total features these alignments represent : 50.71 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 28383
2	 498
3	 79
4	 62
5	 39
6	 35
8	 15
9	 9
10	 6
20	 1
30	 1
40	 2
50	 0
100	 2

 Features that hit more than thrice are deleted.  
# remaining Alignments : 29616
# unique Features these remaining alignments represent: 28960
% of total features these alignments represent : 50.41 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 2
40	 29
50	 38
60	 92
70	 389
80	 2984
90	 21226
95	 4611
100	 245

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 21162
2000	 4337
3000	 1918
4000	 739
5000	 384
6000	 174
7000	 113
8000	 85
9000	 44
10000	 33

Following is the final summary
# alignments : 29616
# unique Features these alignments represent: 28960
% of total features these alignments represent : 50.41 %