This reports the protocol used to align the Maize_HiCotCluster_TIGR features to tigrv4-genome.
Fri Apr 14 18:25:04 2006


Source of Maize_HiCotCluster_TIGR : from Gramene markers database, originally Downloaded from TIGR using the link ftp://ftp.tigr.org/pub/data/MAIZE/AZMs/release_4.0/zmg_fasta.4.0HC_022304.gz 

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

172600 Maize_HiCotCluster_TIGR 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 : 61368
# unique Features these alignments represent: 54399
% of total features these alignments represent : 31.52 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 19600
150	 8601
200	 7028
250	 5406
300	 4036
350	 3312
400	 2623
450	 2086
500	 1697
550	 1308
600	 1046
650	 835
700	 683
750	 574
800	 565
10000	 1968

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 41986
# unique Features these remaining alignments represent: 38056
% of total features these alignments represent : 22.05 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 38840
2000	 1525
3000	 291
4000	 106
5000	 75
6000	 45
7000	 45
8000	 33
9000	 30
10000	 26
20000	 168

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 40762
# unique Features these remaining alignments represent: 36974
% of total features these alignments represent : 21.42 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 35108
2	 1180
3	 217
4	 169
5	 142
6	 68
8	 42
9	 12
10	 17
20	 18
30	 0
40	 1
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 38119
# unique Features these remaining alignments represent: 36505
% of total features these alignments represent : 21.15 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 3
30	 65
40	 275
50	 651
60	 1138
70	 2203
80	 5248
90	 21994
100	 6542

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 36112
# unique Features these remaining alignments represent: 34685
% of total features these alignments represent : 20.10 %

Following is the final summary
# alignments : 36112
# unique Features these alignments represent: 34685
% of total features these alignments represent : 20.10 %