This reports the protocol used to align the Maize_BACend features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 21:27:41 2007


Source of Maize_BACend : Downloaded from genbank with query '(txid4577[orgn] AND Wing[AUTH] AND Messing[AUTH]  AND "BAC ends"[ALL])' 

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

2060913 Maize_BACend 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 : 145426
# unique Features these alignments represent: 104855
% of total features these alignments represent : 5.09 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 94394
150	 10550
200	 4946
250	 3917
300	 2855
350	 2574
400	 2168
450	 2030
500	 1993
550	 2507
600	 2264
650	 2358
700	 2516
750	 2489
800	 1953
10000	 5912

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 51348
# unique Features these remaining alignments represent: 35583
% of total features these alignments represent : 1.73 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 48526
2000	 269
3000	 163
4000	 47
5000	 28
6000	 49
7000	 26
8000	 21
9000	 16
10000	 8
20000	 103

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 49005
# unique Features these remaining alignments represent: 33940
% of total features these alignments represent : 1.65 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 25080
2	 4733
3	 2951
4	 865
5	 202
6	 48
8	 20
9	 5
10	 2
20	 19
30	 14
40	 1
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 43399
# unique Features these remaining alignments represent: 32764
% of total features these alignments represent : 1.59 %

% 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	 43399

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 43399
# unique Features these remaining alignments represent: 32764
% of total features these alignments represent : 1.59 %

Following is the final summary
# alignments : 43399
# unique Features these alignments represent: 32764
% of total features these alignments represent : 1.59 %
  

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