This reports the protocol used to align the Maize_Seq_Panzea features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 14:54:34 2007


Source of Maize_Seq_Panzea : Obtained from panzea project 

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

3092 Maize_Seq_Panzea 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 : 144
# unique Features these alignments represent: 113
% of total features these alignments represent : 3.65 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 88
150	 18
200	 11
250	 8
300	 6
350	 2
400	 1
450	 2
500	 2
550	 1
600	 1
650	 1
700	 1
750	 2
800	 0
10000	 0

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 39
# unique Features these remaining alignments represent: 34
% of total features these alignments represent : 1.10 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 30
2	 3
3	 1
4	 0
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 : 39
# unique Features these remaining alignments represent: 34
% of total features these alignments represent : 1.10 %

% 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	 31
100	 8

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 34
2000	 3
3000	 0
4000	 0
5000	 1
6000	 0
7000	 0
8000	 0
9000	 0
10000	 0

Following is the final summary
# alignments : 39
# unique Features these alignments represent: 34
% of total features these alignments represent : 1.10 %
  

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