This reports the protocol used to align the Rice_Punctata_BACend features to Maize_BACs.
 Kiran Ratnapu 
Mon Mar 28 12:40:12 2005


Source of Rice_Punctata_BACend : Downloaded from genbank nucleotide database using keyword 'OP__Ba'

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

68384 Rice_Punctata_BACend are aligned to Maize_BACs 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 : 10472
# unique Features these alignments represent: 7885
% of total features these alignments represent : 11.53 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 3254
150	 1379
200	 1059
250	 960
300	 678
350	 565
400	 487
450	 451
500	 465
550	 411
600	 350
650	 155
700	 96
750	 79
800	 58
10000	 25

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 7245
# unique Features these remaining alignments represent: 5486
% of total features these alignments represent : 8.02 %

Rice_gap distribution of the remaining features
Rice_gaps	# alignments
--------	--------
1000	 6875
2000	 15
3000	 13
4000	 6
5000	 1
6000	 4
7000	 8
8000	 10
9000	 10
10000	 17
20000	 72

Alignments with gaps on rice > 4000 bp are filtered
# remaining Alignments : 6909
# unique Features these remaining alignments represent: 5278
% of total features these alignments represent : 7.72 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 4310
2	 660
3	 173
4	 52
5	 30
6	 25
8	 12
9	 10
10	 2
20	 4
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 6149
# unique Features these remaining alignments represent: 5143
% of total features these alignments represent : 7.52 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 3
30	 27
40	 109
50	 355
60	 657
70	 954
80	 1397
90	 1603
100	 1044

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 5091
# unique Features these remaining alignments represent: 4206
% of total features these alignments represent : 6.15 %

Following is the final summary
# alignments : 5091
# unique Features these alignments represent: 4206
% of total features these alignments represent : 6.15 %