This reports the protocol used to align the Sorghum_ESTcluster_TIGR features to Maize_BACs_20060126.
Mon Feb 13 15:00:50 2006


Source of Sorghum_ESTcluster_TIGR : Downloaded from TIGR using link ftp://ftp.tigr.org/pub/data/tgi/Sorghum_bicolor/SBGI.release_8.zip 

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

39148 Sorghum_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 : 7378
# unique Features these alignments represent: 5690
% of total features these alignments represent : 14.53 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 1561
150	 937
200	 746
250	 608
300	 543
350	 472
400	 468
450	 385
500	 331
550	 276
600	 190
650	 149
700	 130
750	 80
800	 54
10000	 448

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 4899
# unique Features these remaining alignments represent: 3799
% of total features these alignments represent : 9.70 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 3290
2	 320
3	 40
4	 21
5	 52
6	 47
8	 29
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 4050
# unique Features these remaining alignments represent: 3650
% of total features these alignments represent : 9.32 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 3
50	 5
60	 25
70	 73
80	 227
90	 994
95	 2240
100	 483

Following is the distribution of Gaps
Gaps	# features
--------	--------
1000	 3209
2000	 385
3000	 185
4000	 83
5000	 43
6000	 26
7000	 15
8000	 14
9000	 11
10000	 12

Following is the final summary
# alignments : 4050
# unique Features these alignments represent: 3650
% of total features these alignments represent : 9.32 %