This reports the protocol used to align the Maize_Seq_Panzea features to tigrv4-genome.
Fri Apr 14 11:46:02 2006


Source of Maize_Seq_Panzea : Obtained from panzea project 

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

3092 Maize_Seq_Panzea 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 : 2488
# unique Features these alignments represent: 2432
% of total features these alignments represent : 78.65 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 139
150	 192
200	 235
250	 219
300	 194
350	 223
400	 216
450	 148
500	 123
550	 113
600	 78
650	 72
700	 65
750	 66
800	 63
10000	 342

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 2159
# unique Features these remaining alignments represent: 2121
% of total features these alignments represent : 68.60 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 2096
2	 21
3	 2
4	 1
5	 0
6	 0
8	 0
9	 0
10	 0
20	 1
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 2144
# unique Features these remaining alignments represent: 2119
% of total features these alignments represent : 68.53 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 0
50	 0
60	 2
70	 8
80	 201
90	 1666
95	 263
100	 4

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 1373
2000	 394
3000	 190
4000	 88
5000	 36
6000	 16
7000	 9
8000	 8
9000	 3
10000	 1

Following is the final summary
# alignments : 2144
# unique Features these alignments represent: 2119
% of total features these alignments represent : 68.53 %