This reports the protocol used to align the Barley_ESTcluster_TIGR features to Maize_BACs_20060126.
Mon Feb 13 12:05:55 2006


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

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

50453 Barley_ESTcluster_TIGR 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 : 5674
# unique Features these alignments represent: 4539
% of total features these alignments represent : 9.00 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 1474
150	 825
200	 675
250	 511
300	 454
350	 376
400	 289
450	 302
500	 158
550	 140
600	 68
650	 68
700	 55
750	 46
800	 29
10000	 204

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 3390
# unique Features these remaining alignments represent: 2638
% of total features these alignments represent : 5.23 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 2264
2	 252
3	 24
4	 15
5	 37
6	 30
8	 15
9	 0
10	 0
20	 1
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 2840
# unique Features these remaining alignments represent: 2540
% of total features these alignments represent : 5.03 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 2
40	 1
50	 4
60	 35
70	 88
80	 441
90	 1680
95	 488
100	 101

Following is the distribution of Gaps
Gaps	# features
--------	--------
1000	 2324
2000	 241
3000	 110
4000	 51
5000	 22
6000	 15
7000	 6
8000	 11
9000	 12
10000	 9

Following is the final summary
# alignments : 2840
# unique Features these alignments represent: 2540
% of total features these alignments represent : 5.03 %