This reports the protocol used to align the Barley_EST features to tigrv4-genome.
Fri Apr 14 18:21:06 2006


Source of Barley_EST : from Gramene markers database, originally Downloaded from genbank with query ' txid4512[orgn]  AND  gbdiv_est[PROP]' 

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

419250 Barley_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 : 358211
# unique Features these alignments represent: 297320
% of total features these alignments represent : 70.92 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 27592
150	 32401
200	 38657
250	 39526
300	 40430
350	 39930
400	 38263
450	 32084
500	 22214
550	 17091
600	 13752
650	 8785
700	 4193
750	 1761
800	 1053
10000	 479

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 298931
# unique Features these remaining alignments represent: 241622
% of total features these alignments represent : 57.63 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 219547
2	 9281
3	 3775
4	 3939
5	 1436
6	 1148
8	 2254
9	 192
10	 37
20	 13
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 249434
# unique Features these remaining alignments represent: 232603
% of total features these alignments represent : 55.48 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 1
40	 9
50	 32
60	 368
70	 1300
80	 13301
90	 159040
95	 68250
100	 7133

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 202277
2000	 31304
3000	 6923
4000	 2168
5000	 905
6000	 373
7000	 590
8000	 268
9000	 132
10000	 229

Following is the final summary
# alignments : 249434
# unique Features these alignments represent: 232603
% of total features these alignments represent : 55.48 %