This reports the protocol used to align the Barley_ESTcluster_PlantGDB features to Maize_BACs_20060126.
Mon Feb 13 11:59:59 2006


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

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

84487 Barley_ESTcluster_PlantGDB are aligned to Maize_BACs_20060126 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 : 8610
# unique Features these alignments represent: 7340
% of total features these alignments represent : 8.69 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 2347
150	 1294
200	 1137
250	 958
300	 775
350	 648
400	 488
450	 267
500	 183
550	 123
600	 99
650	 49
700	 48
750	 45
800	 26
10000	 123

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 5000
# unique Features these remaining alignments represent: 4285
% of total features these alignments represent : 5.07 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 3837
2	 354
3	 28
4	 13
5	 18
6	 22
8	 13
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 4629
# unique Features these remaining alignments represent: 4219
% of total features these alignments represent : 4.99 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 2
40	 3
50	 8
60	 33
70	 128
80	 632
90	 2849
95	 810
100	 164

Following is the distribution of Gaps
Gaps	# features
--------	--------
1000	 3982
2000	 330
3000	 137
4000	 60
5000	 21
6000	 18
7000	 6
8000	 15
9000	 15
10000	 9

Following is the final summary
# alignments : 4629
# unique Features these alignments represent: 4219
% of total features these alignments represent : 4.99 %