This reports the protocol used to align the Maize_HiCot_Bennetzen features to tigrv4-genome.
Fri Apr 14 18:27:37 2006


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 tigrv4-genome 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 : 128256
# unique Features these alignments represent: 115753
% of total features these alignments represent : 25.90 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 42889
150	 20604
200	 16448
250	 12630
300	 9308
350	 7217
400	 5217
450	 3937
500	 2824
550	 2034
600	 1469
650	 1088
700	 755
750	 652
800	 578
10000	 606

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 85846
# unique Features these remaining alignments represent: 79048
% of total features these alignments represent : 17.69 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 83532
2000	 396
3000	 100
4000	 72
5000	 85
6000	 74
7000	 55
8000	 58
9000	 33
10000	 35
20000	 242

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 84100
# unique Features these remaining alignments represent: 77534
% of total features these alignments represent : 17.35 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 74149
2	 2207
3	 418
4	 273
5	 234
6	 102
8	 67
9	 26
10	 30
20	 26
30	 1
40	 1
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 79817
# unique Features these remaining alignments represent: 76774
% of total features these alignments represent : 17.18 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 10
30	 95
40	 409
50	 954
60	 1818
70	 3470
80	 10468
90	 47282
100	 15311

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 76749
# unique Features these remaining alignments represent: 73965
% of total features these alignments represent : 16.55 %

Following is the final summary
# alignments : 76749
# unique Features these alignments represent: 73965
% of total features these alignments represent : 16.55 %