This reports the protocol used to align the Sorghum_cDNA features to Maize_BACs_20060126.
Mon Feb 13 14:10:50 2006


Source of Sorghum_cDNA : No description of data source at documentation??? 

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

4720 Sorghum_cDNA 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-Coding' data sets.

Initial summary
# alignments : 596
# unique Features these alignments represent: 542
% of total features these alignments represent : 11.48 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 100
150	 74
200	 76
250	 51
300	 47
350	 54
400	 43
450	 48
500	 33
550	 25
600	 17
650	 4
700	 3
750	 8
800	 5
10000	 8

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 425
# unique Features these remaining alignments represent: 390
% of total features these alignments represent : 8.26 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 356
2	 33
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 : 425
# unique Features these remaining alignments represent: 390
% of total features these alignments represent : 8.26 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 0
50	 0
60	 0
70	 1
80	 9
90	 88
95	 271
100	 56

Following is the distribution of Gaps
Gaps	# features
--------	--------
1000	 355
2000	 39
3000	 15
4000	 6
5000	 1
6000	 1
7000	 2
8000	 0
9000	 1
10000	 0

Following is the final summary
# alignments : 425
# unique Features these alignments represent: 390
% of total features these alignments represent : 8.26 %