This reports the protocol used to align the Maize_MarkerRFLP features to tigrv4-genome.
Tue Apr 25 13:44:41 2006


Source of Maize_MarkerRFLP : The maize RFLP markers pulled out from old Maize_markers dataset, this dataset was obtained from the link http://www.agron.missouri.edu/files_dl/SequenceMap/SequenceMap20030425.txt, unique genbank accessions were pulled out and sequences were extracted from batch entrez 

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

207 Maize_MarkerRFLP 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 : 111
# unique Features these alignments represent: 102
% of total features these alignments represent : 49.28 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 22
150	 33
200	 29
250	 9
300	 8
350	 2
400	 4
450	 0
500	 0
550	 0
600	 1
650	 0
700	 0
750	 1
800	 0
10000	 2

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 57
# unique Features these remaining alignments represent: 50
% of total features these alignments represent : 24.15 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 44
2	 5
3	 1
4	 0
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 : 57
# unique Features these remaining alignments represent: 50
% of total features these alignments represent : 24.15 %

% 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	 41
95	 16
100	 0

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 46
2000	 6
3000	 1
4000	 0
5000	 1
6000	 2
7000	 0
8000	 1
9000	 0
10000	 0

Following is the final summary
# alignments : 57
# unique Features these alignments represent: 50
% of total features these alignments represent : 24.15 %