This reports the protocol used to align the Maize_Marker features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 14:49:21 2007


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 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 : 903
# unique Features these alignments represent: 735
% of total features these alignments represent : 10.55 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 480
150	 87
200	 98
250	 75
300	 51
350	 41
400	 23
450	 25
500	 9
550	 3
600	 3
650	 2
700	 0
750	 0
800	 0
10000	 6

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 336
# unique Features these remaining alignments represent: 298
% of total features these alignments represent : 4.28 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 269
2	 24
3	 1
4	 4
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 thrice are deleted.  
# remaining Alignments : 320
# unique Features these remaining alignments represent: 294
% of total features these alignments represent : 4.22 %

% 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	 121
100	 199

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 281
2000	 25
3000	 5
4000	 2
5000	 0
6000	 3
7000	 0
8000	 0
9000	 0
10000	 0

Following is the final summary
# alignments : 320
# unique Features these alignments represent: 294
% of total features these alignments represent : 4.22 %
  

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