This reports the protocol used to align the Maize_MethylFilter_CSHL features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 15:35:20 2007


Source of Maize_MethylFilter_CSHL : Methyl-filtered CSHL maize sequence, downloaded from genbank with query '(txid4577[ORGN] AND McCombie[AUTH] AND methyl[TITL] AND 2002[MDAT])' 

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

66390 Maize_MethylFilter_CSHL 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 : 10079
# unique Features these alignments represent: 6790
% of total features these alignments represent : 10.23 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 3787
150	 747
200	 451
250	 371
300	 275
350	 333
400	 375
450	 409
500	 391
550	 536
600	 659
650	 676
700	 632
750	 316
800	 105
10000	 16

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 6316
# unique Features these remaining alignments represent: 4229
% of total features these alignments represent : 6.37 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 6114
2000	 50
3000	 29
4000	 8
5000	 1
6000	 14
7000	 5
8000	 1
9000	 1
10000	 0
20000	 12

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 6201
# unique Features these remaining alignments represent: 4159
% of total features these alignments represent : 6.26 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 2899
2	 821
3	 233
4	 103
5	 82
6	 17
8	 3
9	 0
10	 0
20	 1
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 5240
# unique Features these remaining alignments represent: 3953
% of total features these alignments represent : 5.95 %

% 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	 5240

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 5240
# unique Features these remaining alignments represent: 3953
% of total features these alignments represent : 5.95 %

Following is the final summary
# alignments : 5240
# unique Features these alignments represent: 3953
% of total features these alignments represent : 5.95 %
  

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