This reports the protocol used to align the Maize_BACend features to tigrv4-genome.
Fri Apr 14 17:08:53 2006


Source of Maize_BACend : from Gramene markers database, originally Downloaded from genbank with query '(txid4577[orgn] AND Wing[AUTH] AND Messing[AUTH]  AND "BAC ends"[ALL])' 

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

141928 Maize_BACend 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-Genomic' data sets.

Initial summary
# alignments : 64854
# unique Features these alignments represent: 43363
% of total features these alignments represent : 30.55 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 15641
150	 6309
200	 5709
250	 5060
300	 4416
350	 4534
400	 4622
450	 4728
500	 3381
550	 2599
600	 1506
650	 1205
700	 954
750	 1208
800	 637
10000	 2345

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 49365
# unique Features these remaining alignments represent: 31931
% of total features these alignments represent : 22.50 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 46162
2000	 38
3000	 33
4000	 15
5000	 40
6000	 14
7000	 17
8000	 13
9000	 15
10000	 7
20000	 82

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 46248
# unique Features these remaining alignments represent: 29685
% of total features these alignments represent : 20.92 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 22531
2	 3625
3	 940
4	 878
5	 852
6	 680
8	 103
9	 16
10	 16
20	 35
30	 6
40	 3
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 32601
# unique Features these remaining alignments represent: 27096
% of total features these alignments represent : 19.09 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 58
30	 544
40	 1276
50	 1887
60	 3684
70	 10459
80	 8180
90	 4592
100	 1921

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 25760
# unique Features these remaining alignments represent: 21269
% of total features these alignments represent : 14.99 %

Following is the final summary
# alignments : 25760
# unique Features these alignments represent: 21269
% of total features these alignments represent : 14.99 %