This reports the protocol used to align the Rice_Brachyantha_BACend features to Maize_BACs.
 Kiran Ratnapu 
Mon Mar 28 12:25:53 2005


Source of Rice_Brachyantha_BACend : Downloaded from Genbank with 'Brachyantha' as keyword  

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

64604 Rice_Brachyantha_BACend are aligned to Maize_BACs 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 : 7532
# unique Features these alignments represent: 6022
% of total features these alignments represent : 9.32 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 2511
150	 926
200	 684
250	 560
300	 454
350	 447
400	 494
450	 294
500	 362
550	 275
600	 231
650	 115
700	 91
750	 61
800	 21
10000	 6

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 5062
# unique Features these remaining alignments represent: 4008
% of total features these alignments represent : 6.20 %

Rice_gap distribution of the remaining features
Rice_gaps	# alignments
--------	--------
1000	 4690
2000	 9
3000	 2
4000	 1
5000	 1
6000	 4
7000	 7
8000	 6
9000	 9
10000	 7
20000	 24

Alignments with gaps on rice > 4000 bp are filtered
# remaining Alignments : 4702
# unique Features these remaining alignments represent: 3816
% of total features these alignments represent : 5.91 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 3183
2	 506
3	 72
4	 23
5	 12
6	 9
8	 8
9	 2
10	 1
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 4411
# unique Features these remaining alignments represent: 3761
% of total features these alignments represent : 5.82 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 4
40	 54
50	 101
60	 251
70	 665
80	 819
90	 1218
100	 1299

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 4032
# unique Features these remaining alignments represent: 3449
% of total features these alignments represent : 5.34 %

Following is the final summary
# alignments : 4032
# unique Features these alignments represent: 3449
% of total features these alignments represent : 5.34 %