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


Source of Maize_HiCotCluster_TIGR : Downloaded from TIGR using the link ftp://ftp.tigr.org/pub/data/MAIZE/AZMs/release_4.0/zmg_fasta.4.0HC_022304.gz 

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

172600 Maize_HiCotCluster_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 : 11252
# unique Features these alignments represent: 8568
% of total features these alignments represent : 4.96 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 9091
150	 903
200	 310
250	 157
300	 102
350	 100
400	 72
450	 43
500	 36
550	 50
600	 36
650	 37
700	 59
750	 43
800	 71
10000	 142

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 2205
# unique Features these remaining alignments represent: 1733
% of total features these alignments represent : 1.00 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 1823
2000	 25
3000	 16
4000	 7
5000	 3
6000	 5
7000	 2
8000	 3
9000	 3
10000	 1
20000	 21

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 1871
# unique Features these remaining alignments represent: 1465
% of total features these alignments represent : 0.85 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 1238
2	 132
3	 69
4	 18
5	 4
6	 1
8	 0
9	 1
10	 0
20	 0
30	 1
40	 1
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 1709
# unique Features these remaining alignments represent: 1439
% of total features these alignments represent : 0.83 %

% 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	 1709

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 1709
# unique Features these remaining alignments represent: 1439
% of total features these alignments represent : 0.83 %

Following is the final summary
# alignments : 1709
# unique Features these alignments represent: 1439
% of total features these alignments represent : 0.83 %
  

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