BIOBAR : USER MANUAL

IUB characters are considered fractional mismatches depending on
which DNA bases they stand for. For example, B is considered to be 1/3
T, 1/3 G and 1/3 C.
Find Substring with Gap allows the user to search for two substrings
separated by a gap of defined length.
Different Output Locations
BELOW, NEW DOC and CLIPBOARD
o Returns all results
REPLACE
o Highlights the matches in the sequence with a darker color
representing a better scoring sequence
Site Search
o Search (Ri sequence and I sequence)
These Site Search mechanisms can only be completed for DNA sequences.
An error message will be displayed if a protein or RNA sequence is
selected. If sequences of all types are selected, the site search will only
be completed for the DNA sequence(s).
In the motif, only DNA sequences may be entered.
Reports the Ri Score or Iseq Score
o Dyad Pattern Search
Dyad Pattern Search can only be completed for DNA sequences. An error
message will be displayed if a protein or RNA sequence is selected. If
sequences of all types are selected, the site search will only be completed
for the DNA sequence(s).
In the motif, only DNA sequences may be entered.
Different Output Locations:
BELOW, NEW DOC and CLIPBOARD
o Returns all results
REPLACE
o Highlights the dyads in the sequence with a darker color
representing a better scoring sequence
Motif Discovery
o Gibbs Sampling and Greedy Search
Gibbs Sampling can only be completed for DNA sequences. An error
message will be displayed if a protein or RNA sequence is selected. If
sequences of all types are selected, the sampling will only be completed
for the DNA sequence(s).
The program will complete the number of iterations requested 10 times
and return the motif that has the greatest IC content
Different Output Locations:
BELOW, NEW DOC and CLIPBOARD