This reports the protocol used to align the Barley_ESTcluster_TIGR features to tigrv4-genome.
Fri Apr 14 12:00:47 2006


Source of Barley_ESTcluster_TIGR : from Gramene markers database, originally Downloaded from TIGR from the link ftp://ftp.tigr.org/pub/data/tgi/Hordeum_vulgare/HVGI.release_9.zip 

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

46352 Barley_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 : 36508
# unique Features these alignments represent: 17247
% of total features these alignments represent : 37.21 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 2358
150	 2370
200	 3006
250	 2788
300	 3002
350	 2872
400	 2754
450	 2522
500	 2152
550	 1916
600	 1460
650	 1320
700	 1094
750	 998
800	 854
10000	 5042

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 31826
# unique Features these remaining alignments represent: 15037
% of total features these alignments represent : 32.44 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 0
2	 14620
3	 0
4	 256
5	 0
6	 51
8	 25
9	 0
10	 30
20	 54
30	 1
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 29240
# unique Features these remaining alignments represent: 14620
% of total features these alignments represent : 31.54 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 4
50	 12
60	 54
70	 222
80	 2450
90	 21510
95	 4816
100	 172

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 17878
2000	 5612
3000	 2804
4000	 1226
5000	 532
6000	 210
7000	 144
8000	 96
9000	 64
10000	 42

Following is the final summary
# alignments : 29240
# unique Features these alignments represent: 14620
% of total features these alignments represent : 31.54 %