subjects
subject database categories
Can be either whole genomes or sRNAs.
sRNAs are subdivided by organisms.
  cutoffs
homology cutoffs
Here you can set cutoffs for BLAST or/and BOA.
   
available target replicons/sRNAs
subject database
Shows all available genomes or sRNAs sorted
by organism.
Select subjects by clicking; hold
Control/Shift for multiple.
Press "+" to transfer all selected entries to
the selected box.
  BLAST
 
e-value
e-value
This parameter is also known as expect-value.
The probability due to chance, that there is
another alignment with a similarity greater
than the given score. Decrease value for
higher specificity.
match/mismatch
match/mismatch
Ratio that should be increased for the alignment of more
divergent sequences. A ratio of 0.33 (1/-3) is appropriate
for sequences that are about 99% conserved;
a ratio of 0.5 (1/-2) is best for sequences that are 95%
conserved; a ratio of about one (1/-1) is best for sequences
that are 75% conserved. Default ratio set to 0.66 (2/-3).
 
all
selected target replicons
selected subjects
This box shows all selected genomes or sRNAs.
Select subjects by clicking; hold
Control/Shift for multiple.
Press "-" to remove all selected entries
from the selected box.
      BOA
BOA
This feature summarizes the BLAST output.
(homology matrix).
        
 
complete matrix
complete matix
If checked all subjects and queries will be shown
in the matrix.
If unchecked only those subjects and queries will be shown
which have a minimum of one hit. All others
are displayed in a different table.
identity
identity
The extent to which two
sequences are invariant.
query-coverage(min-max)
query-coverage
Determines the min/max percentage of
the query that has to be covered
by the alignment.
-
subject-coverage(min-max)
subject-coverage
Determines the min/max percentage of
the subject that has to be covered
by the alignment.
-