This reports the protocol used to align the Wheat_ESTcluster_TIGR features to tigrv4-genome.
Fri Apr 14 12:03:04 2006


Source of Wheat_ESTcluster_TIGR : from Gramene markers database, originally Downloaded from the TIGR using link ftp://ftp.tigr.org/pub/data/tgi/Triticum_aestivum/TAGI.release_9.zip 

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

44954 Wheat_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 : 31860
# unique Features these alignments represent: 30008
% of total features these alignments represent : 66.75 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 2584
150	 2607
200	 2831
250	 2968
300	 2859
350	 2801
400	 2669
450	 2183
500	 1727
550	 1439
600	 1174
650	 939
700	 794
750	 621
800	 590
10000	 3074

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 26727
# unique Features these remaining alignments represent: 25186
% of total features these alignments represent : 56.03 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 24349
2	 556
3	 99
4	 55
5	 64
6	 36
8	 23
9	 4
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 25758
# unique Features these remaining alignments represent: 25004
% of total features these alignments represent : 55.62 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 1
40	 3
50	 14
60	 27
70	 219
80	 2047
90	 17554
95	 5515
100	 378

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 17438
2000	 4174
3000	 1913
4000	 779
5000	 354
6000	 158
7000	 122
8000	 77
9000	 48
10000	 43

Following is the final summary
# alignments : 25758
# unique Features these alignments represent: 25004
% of total features these alignments represent : 55.62 %