This reports the protocol used to align the Sorghum_ESTcluster_TIGR features to tigrv4-genome.
Fri Apr 14 11:48:20 2006


Source of Sorghum_ESTcluster_TIGR : from Gramene markers database, originally Downloaded from TIGR using link ftp://ftp.tigr.org/pub/data/tgi/Sorghum_bicolor/SBGI.release_8.zip 

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

7996 Sorghum_ESTcluster_TIGR are aligned to tigrv4-genome 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 : 6912
# unique Features these alignments represent: 6266
% of total features these alignments represent : 78.36 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 441
150	 549
200	 689
250	 698
300	 771
350	 843
400	 613
450	 549
500	 387
550	 300
600	 247
650	 188
700	 133
750	 88
800	 85
10000	 331

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 5932
# unique Features these remaining alignments represent: 5384
% of total features these alignments represent : 67.33 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 5172
2	 106
3	 16
4	 29
5	 26
6	 21
8	 5
9	 4
10	 3
20	 2
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 5432
# unique Features these remaining alignments represent: 5294
% of total features these alignments represent : 66.21 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 3
50	 2
60	 5
70	 44
80	 354
90	 3766
95	 1168
100	 90

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 3979
2000	 834
3000	 328
4000	 92
5000	 41
6000	 29
7000	 7
8000	 9
9000	 9
10000	 5

Following is the final summary
# alignments : 5432
# unique Features these alignments represent: 5294
% of total features these alignments represent : 66.21 %