This reports the protocol used to align the Maize_EST features to tigrv4-genome.
Fri Apr 14 19:51:04 2006


Source of Maize_EST : from Gramene markers database, originally Downloaded from genbank with query ' txid4577[orgn]  AND  gbdiv_est[PROP]' 

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

705163 Maize_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 : 484738
# unique Features these alignments represent: 452339
% of total features these alignments represent : 64.15 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 55217
150	 53581
200	 60429
250	 57680
300	 56418
350	 51253
400	 48765
450	 35411
500	 24527
550	 17953
600	 10947
650	 6568
700	 3774
750	 1583
800	 449
10000	 183

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 377288
# unique Features these remaining alignments represent: 350024
% of total features these alignments represent : 49.64 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 335502
2	 9310
3	 2165
4	 1123
5	 846
6	 474
8	 386
9	 77
10	 62
20	 79
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 360617
# unique Features these remaining alignments represent: 346977
% of total features these alignments represent : 49.21 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 2
30	 3
40	 17
50	 84
60	 292
70	 1737
80	 23647
90	 249355
95	 81764
100	 3716

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 293205
2000	 44180
3000	 11590
4000	 3117
5000	 1709
6000	 864
7000	 546
8000	 460
9000	 249
10000	 260

Following is the final summary
# alignments : 360617
# unique Features these alignments represent: 346977
% of total features these alignments represent : 49.21 %