BIOBAR : USER MANUAL

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Only DNA sequences can be used.. An error message will be displayed if a protein or RNA sequence is selected. If both DNA and protein sequences are selected, an error message will be displayed and %GC will only be calculated for the DNA sequence(s). Calculates the %GC content for the entire sequence and displays it in a table. o Window %GC Only DNA sequences can be used.. An error message will be displayed if a protein or RNA sequence is selected. If both DNA and protein sequences are selected, an error message will be displayed and %GC will only be calculated for the DNA sequence(s). Calculates the %GC content for windows of length defined by user in the Sequence Statistics Options and displays them in a table, indexed by position. o Nucleotide Frequencies Only DNA sequences can be used. An error message will be displayed if a protein or RNA sequence is selected. If both DNA and protein sequences are selected, an error message will be displayed and nucleotide frequencies will only be calculated for the DNA sequence(s). Calculates frequency of each nucleotide for the entire sequence and displays it in a table. o N-Gram Only DNA sequences can be used. An error message will be displayed if a protein or RNA sequence is selected. If sequences of all types are selected, the N-Grams will only be calculated for the DNA sequence(s). IUB characters will be ignored Takes the value of N from Sequence Statistics Options and generates a list of all possible “words” of length N (from the characters A, T, C, G) and their counts within the sequence. See Sequence Statistics Options for other options relating to N-Grams o Codon Usage Table Only DNA sequences can be used. An error message will be displayed if a protein or RNA is selected. If sequences of all types are selected, the codon usage table will only be generated for the DNA sequence(s). IUB characters will be ignored Generates a codon usage table (using the offset from Sequence Statistics Options) using the sequence(s) that are selected. See Sequence Statistics Options for options relating to table display o Calculate Molecular Weight Open to DNA, RNA and protein sequences.
See Sequence Statistics Options for options relating to Molecular Weight Protein Sequence Statistics o GRAVY GRAVY can only be calculated for protein sequences. An error message will be displayed if a DNA or RNA sequence is selected. If sequences of all types are selected, GRAVY will only be calculated for protein sequence(s). GRAVY is the average of the hydropathicites of the amino acids. o Isoelectric Point Isoelectric points can only be calculated for protein sequences. An error message will be displayed if a DNA or RNA sequence is selected. If sequences of all types are selected, the isoelectric point will only be generated for protein sequence(s). The isoelectric point is the pH at which the protein carries a zero net electric charge. o Generate Protein Statistics Protein statistics can only be calculated for protein sequences. An error message will be displayed if a DNA or RNA sequence is selected. If sequences of all types are selected, the protein statistics will only be generated for the strict DNA sequence(s). Protein statistics provides a count and percentage of each of the amino acids for each sequence. Substring Search o Find ORFs (Open Reading Frames) ORFs can only be found 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 ORFs will only be found for the DNA sequence(s). ATG, TTG, CTG and GTG are all considered start codons Different Output Locations: BELOW – Only prints the top-scoring ORF REPLACE – Highlights the top-scoring ORF CLIPBOARD – Saves all discovered ORFs NEW DOC – Prints all discovered ORFs See Motif Discovery Options for options relating to ORFs o Find Substring Substring searches 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 substring search will only be completed for the DNA sequence(s).
Page 1 and 2: BIOBAR : USER MANUAL INSTALLING: AU
Page 3 and 4: IUB - for each amino acid in the se
Page 5 and 6: Motif Discovery o Gibbs Sampling %
Page 7: If an incorrect character (not A, T
Page 11: o Returns the best result REPLACE o

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