This reports the protocol used to align the Maize_HiCotMethylFilterCluster_TIGR features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 19:01:41 2007


Source of Maize_HiCotMethylFilterCluster_TIGR : Downloaded from TIGR using the link ftp://ftp.tigr.org/pub/data/MAIZE/AZMs/release_4.0/zmg_fasta.4.0ALL_022304.gz 

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

243807 Maize_HiCotMethylFilterCluster_TIGR 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 : 18176
# unique Features these alignments represent: 12960
% of total features these alignments represent : 5.32 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 14639
150	 1311
200	 446
250	 221
300	 180
350	 149
400	 160
450	 81
500	 86
550	 87
600	 75
650	 86
700	 100
750	 79
800	 124
10000	 352

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 3590
# unique Features these remaining alignments represent: 2575
% of total features these alignments represent : 1.06 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 2912
2000	 85
3000	 38
4000	 19
5000	 9
6000	 5
7000	 3
8000	 2
9000	 10
10000	 2
20000	 26

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 3054
# unique Features these remaining alignments represent: 2137
% of total features these alignments represent : 0.88 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 1678
2	 253
3	 147
4	 41
5	 4
6	 1
8	 2
9	 1
10	 0
20	 2
30	 7
40	 1
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 2625
# unique Features these remaining alignments represent: 2078
% of total features these alignments represent : 0.85 %

% 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	 2625

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 2625
# unique Features these remaining alignments represent: 2078
% of total features these alignments represent : 0.85 %

Following is the final summary
# alignments : 2625
# unique Features these alignments represent: 2078
% of total features these alignments represent : 0.85 %
  

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