This reports the protocol used to align the Maize_ArrayGene_NSF58K features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 15:37:35 2007


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 Oryza_sativa_indica-chromosome-20070724 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 : 3435
# unique Features these alignments represent: 2845
% of total features these alignments represent : 4.95 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 1713
150	 427
200	 277
250	 188
300	 234
350	 85
400	 107
450	 75
500	 59
550	 28
600	 14
650	 18
700	 31
750	 30
800	 16
10000	 133

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 1304
# unique Features these remaining alignments represent: 1025
% of total features these alignments represent : 1.78 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 895
2	 77
3	 31
4	 14
5	 4
6	 1
8	 0
9	 0
10	 0
20	 2
30	 0
40	 0
50	 1
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 1142
# unique Features these remaining alignments represent: 1003
% of total features these alignments represent : 1.75 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 0
50	 0
60	 0
70	 0
80	 0
90	 0
95	 812
100	 330

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 936
2000	 98
3000	 44
4000	 12
5000	 6
6000	 13
7000	 4
8000	 3
9000	 1
10000	 0

Following is the final summary
# alignments : 1142
# unique Features these alignments represent: 1003
% of total features these alignments represent : 1.75 %
  

Last modified: Thu Sep 13 15:01:03 2007