This reports the protocol used to align the Sorghum_GSS_Klein features to Maize_BACs_20060126.
Mon Feb 13 18:50:48 2006


Source of Sorghum_GSS_Klein : These are from Patricia Klein 

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

172 Sorghum_GSS_Klein 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 : 42
# unique Features these alignments represent: 37
% of total features these alignments represent : 21.51 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 13
150	 4
200	 3
250	 2
300	 2
350	 5
400	 4
450	 0
500	 3
550	 1
600	 1
650	 1
700	 3
750	 0
800	 0
10000	 0

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 29
# unique Features these remaining alignments represent: 27
% of total features these alignments represent : 15.70 %

Gap distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 28
2000	 0
3000	 0
4000	 0
5000	 0
6000	 1
7000	 0
8000	 0
9000	 0
10000	 0
20000	 0

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 28
# unique Features these remaining alignments represent: 26
% of total features these alignments represent : 15.12 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 25
2	 0
3	 1
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 : 28
# unique Features these remaining alignments represent: 26
% of total features these alignments represent : 15.12 %

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

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 28
# unique Features these remaining alignments represent: 26
% of total features these alignments represent : 15.12 %

Following is the final summary
# alignments : 28
# unique Features these alignments represent: 26
% of total features these alignments represent : 15.12 %