This reports the protocol used to align the RiceAlta_BACend_OMAP features to Maize_BACs_20060126.
Mon Feb 13 16:49:53 2006


Source of RiceAlta_BACend_OMAP : Downloaded from genbank nucleotide databse with keyword 'OA_BBa'   

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

128732 RiceAlta_BACend_OMAP are aligned to Maize_BACs_20060126 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 : 17049
# unique Features these alignments represent: 12297
% of total features these alignments represent : 9.55 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 4981
150	 2454
200	 1774
250	 1523
300	 1251
350	 1178
400	 1122
450	 811
500	 638
550	 554
600	 359
650	 227
700	 91
750	 53
800	 21
10000	 12

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 12129
# unique Features these remaining alignments represent: 8518
% of total features these alignments represent : 6.62 %

Gap distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 11610
2000	 32
3000	 31
4000	 13
5000	 12
6000	 13
7000	 9
8000	 24
9000	 18
10000	 10
20000	 44

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 11686
# unique Features these remaining alignments represent: 8245
% of total features these alignments represent : 6.40 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 6317
2	 1211
3	 329
4	 203
5	 88
6	 36
8	 43
9	 14
10	 2
20	 2
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 9726
# unique Features these remaining alignments represent: 7857
% of total features these alignments represent : 6.10 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 4
30	 90
40	 193
50	 430
60	 833
70	 1575
80	 2709
90	 2614
100	 1278

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 8275
# unique Features these remaining alignments represent: 6592
% of total features these alignments represent : 5.12 %

Following is the final summary
# alignments : 8275
# unique Features these alignments represent: 6592
% of total features these alignments represent : 5.12 %