This reports the protocol used to align the Maize_ESTcluster_TIGR features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 19:35:05 2007


Source of Maize_ESTcluster_TIGR : Downloaded from tigr with link ftp://ftp.tigr.org/pub/data/tgi/Zea_mays/ZMGI.release_15.zip 

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

31375 Maize_ESTcluster_TIGR are aligned to Oryza_sativa_indica-chromosome-20070724 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 : 1823
# unique Features these alignments represent: 1558
% of total features these alignments represent : 4.97 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 795
150	 233
200	 192
250	 128
300	 101
350	 54
400	 84
450	 48
500	 47
550	 21
600	 10
650	 8
700	 13
750	 12
800	 9
10000	 68

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 801
# unique Features these remaining alignments represent: 662
% of total features these alignments represent : 2.11 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 560
2	 71
3	 25
4	 6
5	 0
6	 0
8	 0
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 777
# unique Features these remaining alignments represent: 656
% of total features these alignments represent : 2.09 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 0
50	 0
60	 0
70	 0
80	 0
90	 0
95	 517
100	 260

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 624
2000	 79
3000	 27
4000	 12
5000	 5
6000	 5
7000	 2
8000	 3
9000	 1
10000	 0

Following is the final summary
# alignments : 777
# unique Features these alignments represent: 656
% of total features these alignments represent : 2.09 %
  

Last modified: Thu Sep 13 15:01:03 2007