This reports the protocol used to align the Barley_ESTcluster_PlantGDB features to tigrv4-genome.
Mon Apr 24 16:36:42 2006


Source of Barley_ESTcluster_PlantGDB : this is a set of  EST clusters and singletons from Gramene markers database, originally down loaded from PlantGDB website.\nhttp://www.plantgdb.org/download/Download/Sequence/ESTcontig/Hordeum_vulgare/Hordeum_vulgare.PUT.fasta.bz2 

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

99915 Barley_ESTcluster_PlantGDB 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 : 63452
# unique Features these alignments represent: 58710
% of total features these alignments represent : 58.76 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 7226
150	 7029
200	 7458
250	 7416
300	 7051
350	 6191
400	 5245
450	 4293
500	 2922
550	 2091
600	 1493
650	 1058
700	 809
750	 581
800	 461
10000	 2128

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 49340
# unique Features these remaining alignments represent: 45477
% of total features these alignments represent : 45.52 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 43682
2	 1102
3	 242
4	 142
5	 75
6	 54
8	 141
9	 32
10	 4
20	 3
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 46612
# unique Features these remaining alignments represent: 45026
% of total features these alignments represent : 45.06 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 8
50	 17
60	 98
70	 379
80	 3862
90	 31866
95	 9779
100	 603

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 35688
2000	 6183
3000	 2128
4000	 831
5000	 336
6000	 156
7000	 141
8000	 73
9000	 58
10000	 45

Following is the final summary
# alignments : 46612
# unique Features these alignments represent: 45026
% of total features these alignments represent : 45.06 %