This reports the protocol used to align the Rice_ESTcluster_PlantGDB features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 18:40:34 2007


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

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

141239 Rice_ESTcluster_PlantGDB are aligned to Oryza_sativa_indica-chromosome-20070724 using blat with blat parameters -minScore=120 followed by PslReps with -singleHit. This was followed by a filtering procedure described below and applied in general to 'Coding-SameSpecies' data sets.

Initial summary
# alignments : 117657
# unique Features these alignments represent: 113911
% of total features these alignments represent : 80.65 %

The following is the distribution of the feature coverage 
%coverage	no of alignments
--------	--------
9	 23
19	 244
29	 714
39	 1424
49	 2531
59	 5296
69	 8808
79	 8683
89	 13987
90	 2479
91	 2683
92	 3122
93	 3826
94	 4877
95	 5992
96	 7277
97	 8504
98	 9519
99	 10100
100	 17567

 Alignments less than 95 % coverage are deleted
# remaining Alignments : 53060
# unique Features these remaining alignments represent: 51718
% of total features these alignments represent : 36.62 %

GAP distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 36425
2000	 7360
3000	 3899
4000	 1913
5000	 997
6000	 593
7000	 360
8000	 240
9000	 178
10000	 125
20000	 509

Alignments with gaps > 4000 bp are deleted
# remaining Alignments : 49597
# unique Features these remaining alignments represent: 48303
% of total features these alignments represent : 34.20 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 0
92	 0
93	 0
94	 59
95	 448
96	 1023
97	 2462
98	 7607
99	 30216
100	 7782

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 47207
2	 1029
3	 40
4	 11
5	 4
6	 2
8	 2
9	 2
10	 1
20	 2
30	 3
40	 0
50	 0
100	 0

 Features that hit more than four times are deleted.  
# remaining Alignments : 49429
# unique Features these remaining alignments represent: 48287
% of total features these alignments represent : 34.19 %
  

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