This reports the protocol used to align the Rice_Ds_Insert features to Maize_BACs.
 Kiran Ratnapu 
Mon Mar 28 12:06:54 2005


Source of Rice_Ds_Insert : Downloaded from Genbank with query "txid4530[orgn] AND GSS[PROP] AND Ds insertion lines"  

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

2058 Rice_Ds_Insert 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 : 98
# unique Features these alignments represent: 80
% of total features these alignments represent : 3.89 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 47
150	 15
200	 12
250	 18
300	 6
350	 0
400	 0
450	 0
500	 0
550	 0
600	 0
650	 0
700	 0
750	 0
800	 0
10000	 0

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 51
# unique Features these remaining alignments represent: 42
% of total features these alignments represent : 2.04 %

Rice_gap distribution of the remaining features
Rice_gaps	# alignments
--------	--------
1000	 51
2000	 0
3000	 0
4000	 0
5000	 0
6000	 0
7000	 0
8000	 0
9000	 0
10000	 0
20000	 0

Alignments with gaps on rice > 4000 bp are filtered
# remaining Alignments : 51
# unique Features these remaining alignments represent: 42
% of total features these alignments represent : 2.04 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 33
2	 9
3	 0
4	 0
5	 0
6	 0
8	 0
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 51
# unique Features these remaining alignments represent: 42
% of total features these alignments represent : 2.04 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 0
40	 1
50	 0
60	 3
70	 11
80	 4
90	 7
100	 25

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 47
# unique Features these remaining alignments represent: 38
% of total features these alignments represent : 1.85 %

Following is the final summary
# alignments : 47
# unique Features these alignments represent: 38
% of total features these alignments represent : 1.85 %