This reports the protocol used to align the Maize_HiCot_Bennetzen features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 19:19:13 2007


Source of Maize_HiCot_Bennetzen : Downloaded from Genbank with query '(txid4577[ORGN] AND Bennetzen[AUTH] AND Cot[ALL])' 

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

446926 Maize_HiCot_Bennetzen 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 : 23715
# unique Features these alignments represent: 18805
% of total features these alignments represent : 4.21 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 19188
150	 2017
200	 647
250	 323
300	 272
350	 207
400	 139
450	 115
500	 75
550	 76
600	 60
650	 82
700	 90
750	 96
800	 135
10000	 193

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 4600
# unique Features these remaining alignments represent: 3702
% of total features these alignments represent : 0.83 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 4082
2000	 25
3000	 26
4000	 10
5000	 3
6000	 15
7000	 6
8000	 2
9000	 6
10000	 0
20000	 19

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 4143
# unique Features these remaining alignments represent: 3350
% of total features these alignments represent : 0.75 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 2877
2	 307
3	 113
4	 32
5	 10
6	 4
8	 1
9	 3
10	 0
20	 0
30	 2
40	 1
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 3830
# unique Features these remaining alignments represent: 3297
% of total features these alignments represent : 0.74 %

% 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	 3830

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 3830
# unique Features these remaining alignments represent: 3297
% of total features these alignments represent : 0.74 %

Following is the final summary
# alignments : 3830
# unique Features these alignments represent: 3297
% of total features these alignments represent : 0.74 %
  

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