BIOBAR : USER MANUAL

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FUNCTIONALITY : Basic Manipulation o Convert Sequence To: Raw – The sequence(s) selected will be printed in the raw format FASTA – The sequence(s) selected will be printed in FASTA format A default header (> # Default) will be created if one is not provided (> # [user input]) GenBank – The sequence(s) selected will be printed in GenBank format o Reverse DNA, RNA and protein sequences can be reversed ATAGTAGAT -> TAGATGATA o Complement Only DNA and RNA sequences may be complemented. An error message will be displayed if a protein sequence is selected. If DNA, RNA, and protein sequences are selected, an error message will be displayed and only the DNA and RNA sequence(s) will be complemented. IUB characters will be ignored. ATAGTAGAT -> TATCATCTA o Reverse Complement Only DNA and RNA sequences may be complemented. An error message will be displayed if a protein sequence is selected. If DNA, RNA and protein sequences are selected, an error message will be displayed and only the DNA and RNA sequence(s) will be reverse complemented. IUB characters will be ignored. ATAGTAGAT -> ATCTACTAT Translation o Forward (Translation) Only DNA sequences may be translated. An error message will be displayed if a protein sequence is selected. If DNA, RNA and protein sequences are selected, an error message will be displayed and only the DNA sequence(s) will be translated. If IUB is selected: Due to possible duplicities with IUB code, a list of all codons corresponding to that IUB code will be generated and a random one will be chosen to be used in translation o Example: GCode = Standard: TGB -> [TGC, TGT, TGG] -> C or W
If an incorrect character (not A, T, C, G, R, Y, M, K, S, W, H, B, V, D, N) is found, an error message will be displayed and translation will not occur Translation will be performed according to the default Genetic Code selected and according to the offset specified in Translation Options NOTE: additional bases will be removed Examples: (italicized characters are ignored) Offset = 0, GCode = Standard: ATAGTAGAT -> IVD Offset =1, GCode = Standard: ATAGTAGAT -> ** o Reverse (Translation) Only protein sequences may be reverse translated. An error message will be displayed if a DNA or RNA sequence is selected. If DNA, RNA and protein sequences are selected, an error message will be displayed and only the protein sequence(s) will be reverse translated. Reverse Translation will be performed according to the method specified in the Reverse Translation/Translation Options If the user provides a Codon Usage Table, the reverse translation will occur according to the Codon Usage Table rather than the default Genetic Code Examples: o GCode = Standard: IVD -> ATAGTAGAT o (Translation) Map Only DNA sequences can be used to create a translation map. An error message will be displayed if a protein or RNA sequence is selected. If DNA, RNA, and protein sequences are selected, an error message will be displayed and translation maps will only be displayed for the DNA sequence(s). The sequence(s) is (are) translated for each of the frames and all of the resultant sequences are displayed together. If IUB is selected: Due to possible duplicities with IUB code, a list of all codons corresponding to that IUB code will be generated and a random one will be chosen to be used in translation o Example: GCode = Standard: TGB -> [TGC, TGT, TGG] -> C or W If an incorrect character (not A, T, C, G, R, Y, M, K, S, W, H, B, V, D, N) is found, an error message will be displayed and translation will not occur DNA Sequence Statistics o Global %GC
Page 1 and 2: BIOBAR : USER MANUAL INSTALLING: AU
Page 3 and 4: IUB - for each amino acid in the se
Page 5: Motif Discovery o Gibbs Sampling %
Page 9 and 10: See Sequence Statistics Options for
Page 11: o Returns the best result REPLACE o

BIOBAR : USER MANUAL

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