This reports the protocol used to align the Maize_MethylFilter_Orion features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 19:39:15 2007


Source of Maize_MethylFilter_Orion : Methyl-filtered TIGR maize sequence, downloaded from genbank with query '(txid4577[ORGN] AND Quackenbush[AUTH] AND "methylation"[ALL] )' 

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

450197 Maize_MethylFilter_Orion 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 : 30567
# unique Features these alignments represent: 23566
% of total features these alignments represent : 5.23 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 23459
150	 2790
200	 1219
250	 697
300	 470
350	 342
400	 295
450	 208
500	 136
550	 138
600	 107
650	 102
700	 116
750	 120
800	 127
10000	 241

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 7204
# unique Features these remaining alignments represent: 6058
% of total features these alignments represent : 1.35 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 6571
2000	 58
3000	 43
4000	 10
5000	 9
6000	 7
7000	 2
8000	 4
9000	 5
10000	 3
20000	 28

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 6682
# unique Features these remaining alignments represent: 5622
% of total features these alignments represent : 1.25 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 5024
2	 387
3	 137
4	 46
5	 9
6	 5
8	 3
9	 1
10	 0
20	 5
30	 5
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 6209
# unique Features these remaining alignments represent: 5548
% of total features these alignments represent : 1.23 %

% 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	 6209

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 6209
# unique Features these remaining alignments represent: 5548
% of total features these alignments represent : 1.23 %

Following is the final summary
# alignments : 6209
# unique Features these alignments represent: 5548
% of total features these alignments represent : 1.23 %
  

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