This reports the protocol used to align the Maize_MAGI_ISU features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 19:26:09 2007


Source of Maize_MAGI_ISU : Maize_ISU_MAGIs_3_1_w_singleton : Downloaded from http://magi.plantgenomics.iastate.edu/downloadall.html 

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

192954 Maize_MAGI_ISU 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-Genomic' data sets.

Initial summary
# alignments : 11198
# unique Features these alignments represent: 8823
% of total features these alignments represent : 4.57 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 9696
150	 847
200	 251
250	 129
300	 68
350	 63
400	 36
450	 31
500	 17
550	 15
600	 13
650	 7
700	 7
750	 3
800	 1
10000	 14

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 1543
# unique Features these remaining alignments represent: 1377
% of total features these alignments represent : 0.71 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 1131
2000	 37
3000	 13
4000	 6
5000	 8
6000	 6
7000	 2
8000	 2
9000	 8
10000	 8
20000	 15

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 1187
# unique Features these remaining alignments represent: 1075
% of total features these alignments represent : 0.56 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 1010
2	 48
3	 8
4	 3
5	 1
6	 0
8	 4
9	 0
10	 1
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 1130
# unique Features these remaining alignments represent: 1066
% of total features these alignments represent : 0.55 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 0
40	 0
50	 0
60	 0
70	 0
80	 0
90	 0
100	 1130

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 1130
# unique Features these remaining alignments represent: 1066
% of total features these alignments represent : 0.55 %

Following is the final summary
# alignments : 1130
# unique Features these alignments represent: 1066
% of total features these alignments represent : 0.55 %
  

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