BIOBAR : USER MANUAL

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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
IUB - for each amino acid in the sequence, its IUB code will be used If checked, user will be prompted to enter a Codon Usage Table after the Reverse Translation button has been pressed, which will be used in reverse translation. The following additional options are allowed: Best - for each amino acid in the sequence(s), the codon with the highest frequency associated with that amino acid (determined by Codon Usage Table) will be selected Random Best - for each amino acid in the sequence(s), a random number will be generated and a codon associated with that amino acid will be selected relative to its frequency (determined by Codon Usage Table) NOTE: Please use the codon usage tables found on http://www.kazusa.or.jp/codon/ using the option for “a style like CodonFrequency output in GCG” DNA Statistics Options o Window-Based % GC Length – this value will serve as the sliding window length when calculating % GC Step-size – the value will serve as the number of base-pairs the sliding window shifts each time (useful for long sequences) o N-Gram The user-entered value will serve as n (the length of each “gram”) Only display N-Grams found in the sequence With this option selected, only N-Grams with a nonzero count will be displayed in the table. o If ATAG were selected, with n = 2, only AT, TA, AG will be displayed in the table rather than AA, AC, AG, AT,…,TT Include the reverse complement With this option selected, the counts of N-Grams of the reverse complement will be added to the counts of the original sequence o Molecular Weight Consider DNA sequences double stranded Include a 5’ triphosphate on RNA sequences Include a 5’ monophosphate on DNA sequences o Codon Usage Table Offset Refers to the frame (0, +1, +2) Table Display
Page 1: BIOBAR : USER MANUAL INSTALLING: AU
Page 5 and 6: Motif Discovery o Gibbs Sampling %
Page 7 and 8: If an incorrect character (not A, T
Page 9 and 10: See Sequence Statistics Options for
Page 11: o Returns the best result REPLACE o

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