This reports the protocol used to align the Maize_ESTcluster_MMPconsensus features to tigrv4-genome.
Fri Apr 14 11:49:21 2006


Source of Maize_ESTcluster_MMPconsensus : MaizeDB Unigenes, these are obtained from Mary Polacco ??? 

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

10678 Maize_ESTcluster_MMPconsensus are aligned to tigrv4-genome 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 : 8286
# unique Features these alignments represent: 8111
% of total features these alignments represent : 75.96 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 630
150	 744
200	 871
250	 841
300	 752
350	 693
400	 620
450	 487
500	 409
550	 308
600	 243
650	 233
700	 194
750	 196
800	 142
10000	 923

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 6934
# unique Features these remaining alignments represent: 6805
% of total features these alignments represent : 63.73 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 6701
2	 95
3	 4
4	 2
5	 0
6	 2
8	 0
9	 0
10	 0
20	 1
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 6903
# unique Features these remaining alignments represent: 6800
% of total features these alignments represent : 63.68 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 1
50	 1
60	 4
70	 36
80	 531
90	 5274
95	 1028
100	 28

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 4322
2000	 1331
3000	 657
4000	 271
5000	 110
6000	 47
7000	 35
8000	 19
9000	 15
10000	 11

Following is the final summary
# alignments : 6903
# unique Features these alignments represent: 6800
% of total features these alignments represent : 63.68 %