This reports the protocol used to align the Maize_EST features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 22:13:07 2007


Source of Maize_EST : Downloaded from genbank with query ' txid4577[orgn]  AND  gbdiv_est[PROP]' 

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

1163689 Maize_EST 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 : 119628
# unique Features these alignments represent: 94651
% of total features these alignments represent : 8.13 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 66934
150	 19882
200	 7750
250	 4500
300	 4980
350	 3613
400	 4150
450	 2449
500	 1459
550	 1380
600	 879
650	 584
700	 451
750	 375
800	 162
10000	 80

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 33035
# unique Features these remaining alignments represent: 27691
% of total features these alignments represent : 2.38 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 23927
2	 2645
3	 779
4	 266
5	 53
6	 13
8	 7
9	 0
10	 0
20	 0
30	 1
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 31554
# unique Features these remaining alignments represent: 27351
% of total features these alignments represent : 2.35 %

% 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	 23769
100	 7785

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 24658
2000	 2930
3000	 908
4000	 174
5000	 46
6000	 325
7000	 28
8000	 186
9000	 18
10000	 2

Following is the final summary
# alignments : 31554
# unique Features these alignments represent: 27351
% of total features these alignments represent : 2.35 %
  

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