This reports the protocol used to align the Sorghum_EST features to tigrv4-genome.
Fri Apr 14 18:08:18 2006


Source of Sorghum_EST : from Gramene markers database, originally Downloaded from genbank with query ' txid4557[orgn]  AND  gbdiv_est[PROP]' 

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

232284 Sorghum_EST 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 : 186281
# unique Features these alignments represent: 167835
% of total features these alignments represent : 72.25 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 15789
150	 17971
200	 21693
250	 23017
300	 23152
350	 22088
400	 20020
450	 15732
500	 10804
550	 7553
600	 4334
650	 2462
700	 1118
750	 331
800	 141
10000	 76

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 152888
# unique Features these remaining alignments represent: 136371
% of total features these alignments represent : 58.71 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 129181
2	 4008
3	 806
4	 938
5	 592
6	 409
8	 148
9	 64
10	 129
20	 96
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 139615
# unique Features these remaining alignments represent: 133995
% of total features these alignments represent : 57.69 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 6
50	 29
60	 131
70	 929
80	 9154
90	 90738
95	 37108
100	 1520

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 115573
2000	 15181
3000	 3554
4000	 1007
5000	 445
6000	 330
7000	 369
8000	 292
9000	 138
10000	 84

Following is the final summary
# alignments : 139615
# unique Features these alignments represent: 133995
% of total features these alignments represent : 57.69 %