This reports the protocol used to align the Rice_transposon_insert_site features to Maize_BACs.
 Kiran Ratnapu 
Mon Mar 28 12:05:21 2005


Source of Rice_transposon_insert_site : Add source  

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

1191 Rice_transposon_insert_site 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 : 47
# unique Features these alignments represent: 39
% of total features these alignments represent : 3.27 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 29
150	 5
200	 7
250	 1
300	 5
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 : 18
# unique Features these remaining alignments represent: 18
% of total features these alignments represent : 1.51 %

Rice_gap distribution of the remaining features
Rice_gaps	# alignments
--------	--------
1000	 18
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 : 18
# unique Features these remaining alignments represent: 18
% of total features these alignments represent : 1.51 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 18
2	 0
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 : 18
# unique Features these remaining alignments represent: 18
% of total features these alignments represent : 1.51 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 0
40	 1
50	 0
60	 0
70	 6
80	 2
90	 5
100	 4

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 17
# unique Features these remaining alignments represent: 17
% of total features these alignments represent : 1.43 %

Following is the final summary
# alignments : 17
# unique Features these alignments represent: 17
% of total features these alignments represent : 1.43 %