This reports the protocol used to align the RiceJaponica_BACend_OMAP features to Maize_BACs_20060126.
Mon Feb 13 23:47:16 2006


Source of RiceJaponica_BACend_OMAP : Downloaded from genbank using the query '(CUGI Rice BAC end) AND (oryza [ORGN])' and only high quality sequence is extracted based on the information from genbank records   

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

88427 RiceJaponica_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 : 32036
# unique Features these alignments represent: 18311
% of total features these alignments represent : 20.71 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 19332
150	 1403
200	 1258
250	 1502
300	 1538
350	 1823
400	 1649
450	 895
500	 1067
550	 251
600	 277
650	 322
700	 313
750	 154
800	 25
10000	 225

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 12735
# unique Features these remaining alignments represent: 7383
% of total features these alignments represent : 8.35 %

Gap distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 11791
2000	 56
3000	 63
4000	 46
5000	 44
6000	 6
7000	 14
8000	 11
9000	 11
10000	 7
20000	 41

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 11956
# unique Features these remaining alignments represent: 6738
% of total features these alignments represent : 7.62 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 5063
2	 788
3	 143
4	 74
5	 147
6	 122
8	 382
9	 13
10	 3
20	 3
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 7068
# unique Features these remaining alignments represent: 5994
% of total features these alignments represent : 6.78 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 2
30	 24
40	 89
50	 235
60	 498
70	 848
80	 988
90	 1697
100	 2687

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 6289
# unique Features these remaining alignments represent: 5304
% of total features these alignments represent : 6.00 %

Following is the final summary
# alignments : 6289
# unique Features these alignments represent: 5304
% of total features these alignments represent : 6.00 %