This reports the protocol used to align the Rice_FSTtransposon features to Maize_BACs_20060126.
Mon Feb 13 18:27:12 2006


Source of Rice_FSTtransposon : UCD FSTs downloaded from genebank using "transposon AND insertion lines AND oryza[Organism]"   

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

3628 Rice_FSTtransposon 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 : 183
# unique Features these alignments represent: 162
% of total features these alignments represent : 4.47 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 90
150	 28
200	 41
250	 13
300	 7
350	 2
400	 2
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 : 93
# unique Features these remaining alignments represent: 75
% of total features these alignments represent : 2.07 %

Gap distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 92
2000	 0
3000	 0
4000	 0
5000	 0
6000	 0
7000	 0
8000	 0
9000	 0
10000	 1
20000	 0

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 92
# unique Features these remaining alignments represent: 74
% of total features these alignments represent : 2.04 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 65
2	 2
3	 6
4	 0
5	 1
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 : 87
# unique Features these remaining alignments represent: 73
% of total features these alignments represent : 2.01 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 0
40	 1
50	 0
60	 5
70	 14
80	 15
90	 24
100	 28

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 81
# unique Features these remaining alignments represent: 67
% of total features these alignments represent : 1.85 %

Following is the final summary
# alignments : 81
# unique Features these alignments represent: 67
% of total features these alignments represent : 1.85 %