This reports the protocol used to align the Maize_ESTcluster_MMPcornsensus features to Rice_Genome(TIGR Version 3).
  
Fri Sep  2 23:50:08 2005


Source of Maize_ESTcluster_MMPcornsensus : These are obtained from Mary Polacco  

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

10678 Maize_ESTcluster_MMPcornsensus are aligned to Rice_Genome(TIGR Version 3) 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 : 8249
# unique Features these alignments represent: 8105
% of total features these alignments represent : 75.90 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 618
150	 735
200	 846
250	 840
300	 774
350	 697
400	 618
450	 481
500	 420
550	 297
600	 253
650	 252
700	 188
750	 156
800	 141
10000	 933

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 6917
# unique Features these remaining alignments represent: 6792
% of total features these alignments represent : 63.61 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 6691
2	 91
3	 7
4	 1
5	 0
6	 0
8	 1
9	 0
10	 0
20	 1
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 6894
# unique Features these remaining alignments represent: 6789
% of total features these alignments represent : 63.58 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 0
50	 2
60	 7
70	 43
80	 522
90	 5289
95	 1003
100	 28

Following is the distribution of Rice gaps
Rice_Gaps	# features
--------	--------
1000	 4303
2000	 1398
3000	 649
4000	 245
5000	 110
6000	 43
7000	 38
8000	 18
9000	 12
10000	 11

Following is the final summary
# alignments : 6894
# unique Features these alignments represent: 6789
% of total features these alignments represent : 63.58 %