This reports the protocol used to align the Sugarcane_EST features to tigrv4-genome.
Fri Apr 14 18:15:59 2006


Source of Sugarcane_EST : from Gramene markers database, originally Downloaded from genbank dbEST with query 'saccharum AND gbdiv_est[PROP]' 

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

255964 Sugarcane_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 : 193325
# unique Features these alignments represent: 182755
% of total features these alignments represent : 71.40 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 15565
150	 16412
200	 19903
250	 21757
300	 21913
350	 22680
400	 22111
450	 19113
500	 14406
550	 10193
600	 6011
650	 2285
700	 655
750	 215
800	 50
10000	 56

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 161708
# unique Features these remaining alignments represent: 152839
% of total features these alignments represent : 59.71 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 147365
2	 4092
3	 636
4	 318
5	 110
6	 90
8	 160
9	 29
10	 25
20	 14
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 157457
# unique Features these remaining alignments represent: 152093
% of total features these alignments represent : 59.42 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 1
30	 2
40	 13
50	 44
60	 154
70	 833
80	 9022
90	 104804
95	 40349
100	 2235

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 126007
2000	 21469
3000	 5244
4000	 1209
5000	 563
6000	 334
7000	 246
8000	 269
9000	 98
10000	 90

Following is the final summary
# alignments : 157457
# unique Features these alignments represent: 152093
% of total features these alignments represent : 59.42 %