BIOBAR : USER MANUAL

White-space-the table will be displayed in the same form as the
codon usage tables from http://www.kazusa.or.jp/codon/
Table-the table will be displayed in a Microsoft Word table
Substring Search Options
o ORF
Minimum codon length – defines the minimum length of an open reading
frame to be reported
o Optimize based on:
Length - when selected, longer ORFs will be ranked higher
CAI and Length – when selected, CAI scores are also taken into
consideration in ranking ORFs
o For Substring and Substring with Gap
Mismatch Threshold – only sequences with less mismatches than the
value entered will be displayed
Site Search
o Ri and Iseq Scoring Options
% GC of Genome– this value will be used to calculate the composition of
the genome sequence that the motif is scored upon
Motif – enter a motif of sequences, all the same length in either Raw or
FASTA format
o Dyad Pattern Search
% GC of Genome – this value will be used to calculate the composition of
the genome sequence that the motif is scored upon
Motif – enter a motif of sequences, all the same length in either Raw or
FASTA format
Threshold - each dyad found must have a score higher than a userdefined
constant times the information content of the motif to be
reported
Gap – defines the range of base-pairs as a spacer between two dyads
For second dyad:
Mirror Motif – when selected, the other half of the dyad will be the
reverse complement of the motif entered
Duplicate Motif – when selected, the other half of the dyad will be
the same as the motif entered
o Consensus Logo
% GC of Genome – this value will be used to calculate the composition of
the genome sequence that the motif is scored upon
Use IUB for equally probably bases – if this option is checked, IUB
characters will be used for two bases that occur at equal frequencies in a
position in the motif. For example, if “A” and “G” are equally likely, “R”
will be used for that position