BIOBAR : USER MANUAL

o % ATCG for DNA
This represents the percentage of A’s, T’s, C’s and G’s that must be in a
sequence for it to be considered DNA
NOTE: the percentage must be entered as an integer, so enter 70 for
70%, NOT 0.7
o Allow IUB Code
If checked, the following IUB characters are allowed in DNA sequences:
A, T, C, G, R, Y, M, K, S, W, H, B, V, D, N
Characters other than the above are filtered out
If not checked, the following characters are allowed in DNA sequences
A, T, C, G
Whether a sequence is DNA or Protein is determined by % ATCG
Characters other than A, T, C or G are filtered out
o If “ATGAAMGA” were selected, “ATGAAGA” would be
processed
o Pseudocounts
LaPlace: pseudocounts for the PSFM calculated using LaPlace’s method
10^-50: pseudocounts intended only to avoid 0 values for log
calculations
Translation Options
o Offset
Refers to the frame of translation (0, +1, +2)
o Genetic Code (GCode)
Denotes the genetic code used in translation and reverse translation
Standard
Vertebrate Mitochondrial
Yeast Mitochondrial
Mold, Protozoan and Coelenterate Mitochondrial/Mycoplasma
and Spiroplasma Mitochondrial
Invertebrate Mitochondrial
Ciliate, Dasycladacean and Hexamita Nuclear
Echinoderm and Flatworm Mitochondrial
Euplotid Mitochondrial
Bacterial, Archaeal and Plant Plasmid
NOTE: this option is overridden if a Codon Usage Table is entered
o Codon Usage Table
If not checked, the default Genetic Code selected will be used in reverse
translation. The following options are allowed:
Uniform - for each amino acid in the sequence(s), a random codon
will be chosen from those associated with that amino acid