This reports the protocol used to align the Rice_FST-TDNA features to Maize_BACs_20060126.
Mon Feb 13 18:36:11 2006


Source of Rice_FST-TDNA : Downloaded from Genbank with query "txid4530[orgn] AND GSS[PROP] AND T-DNA insertion lines" 

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

7480 Rice_FST-TDNA are aligned to Maize_BACs_20060126 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 : 209
# unique Features these alignments represent: 165
% of total features these alignments represent : 2.21 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 126
150	 21
200	 17
250	 18
300	 8
350	 9
400	 9
450	 1
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 : 84
# unique Features these remaining alignments represent: 51
% of total features these alignments represent : 0.68 %

Gap distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 83
2000	 0
3000	 0
4000	 0
5000	 0
6000	 0
7000	 0
8000	 0
9000	 0
10000	 0
20000	 1

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 83
# unique Features these remaining alignments represent: 50
% of total features these alignments represent : 0.67 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 39
2	 4
3	 1
4	 3
5	 1
6	 0
8	 2
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 50
# unique Features these remaining alignments represent: 44
% of total features these alignments represent : 0.59 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 0
40	 0
50	 0
60	 4
70	 8
80	 8
90	 21
100	 9

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 47
# unique Features these remaining alignments represent: 41
% of total features these alignments represent : 0.55 %

Following is the final summary
# alignments : 47
# unique Features these alignments represent: 41
% of total features these alignments represent : 0.55 %