This reports the protocol used to align the Maize_ESTcluster_PlantGDB features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 19:32:39 2007


Source of Maize_ESTcluster_PlantGDB : this is a set of  EST clusters and singletons down loaded from PlantGDB website.\nhttp://www.plantgdb.org/download/Download/Sequence/ESTcontig/Zea_mays/Zea_mays.PUT.fasta.bz2 

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

129494 Maize_ESTcluster_PlantGDB 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 : 13928
# unique Features these alignments represent: 12310
% of total features these alignments represent : 9.51 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 7167
150	 4049
200	 1259
250	 398
300	 292
350	 177
400	 157
450	 102
500	 64
550	 45
600	 32
650	 25
700	 42
750	 29
800	 23
10000	 67

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 2756
# unique Features these remaining alignments represent: 2452
% of total features these alignments represent : 1.89 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 2230
2	 160
3	 45
4	 14
5	 3
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 : 2685
# unique Features these remaining alignments represent: 2435
% of total features these alignments represent : 1.88 %

% 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	 1514
100	 1171

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 1560
2000	 221
3000	 57
4000	 14
5000	 6
6000	 14
7000	 2
8000	 9
9000	 3
10000	 0

Following is the final summary
# alignments : 2685
# unique Features these alignments represent: 2435
% of total features these alignments represent : 1.88 %
  

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