Interfaces
Table of Contents
Interfaces
- AlternateGeneticCodeTranslatorInterface
- Interface AlternateGeneticCodeTranslatorInterface - translates a codon under a specific NCBI
genetic code table (see GeneticCodeTable::SUPPORTED_TABLES). Only the single-letter amino acid
output SequenceInterface::translateCodon()'s format=1 already uses is supported here ; the
3-letter format has no current caller and was left out to keep this service's scope tight.
- ChaosGameRepresentationInterface
- Interface ChaosGameRepresentationInterface - the computation behind a CGR and an FCGR image, with no
drawing : the points of the chaos game, and the counts of the oligonucleotides on their grid.
- CodonAdaptationIndexInterface
- Interface CodonAdaptationIndexInterface - scores how well a coding sequence's own codon choices
match a reference organism's preferred codons (Sharp & Li, 1987), useful for predicting or
optimizing how well a cloned insert is likely to express in a given host.
- CodonOptimizerInterface
- Interface CodonOptimizerInterface - the inverse of CodonAdaptationIndexCalculator : rather than
scoring an existing coding sequence against a reference codon usage table, this picks, for each
residue of a target protein, the synonymous codon with the highest count in that table - the
coding sequence a perfect (CAI = 1) translation of the protein would have.
- CodonUsageTableBuilderInterface
- Interface CodonUsageTableBuilderInterface - builds a CodonUsageTable by counting codon occurrences
across a set of real coding sequences (typically the highly expressed genes of a host organism).
- CpGIslandFinderInterface
- Interface CpGIslandFinderInterface - finds CpG islands using the classic Gardiner-Garden & Frommer
(1987) criteria : GC content and observed/expected CpG ratio both above a threshold, over a
sliding window.
- MeltingTemperatureInterface
- Interface MeltingTemperatureInterface
- OligosInterface
- Interface OligosInterface
- OrfFinderInterface
- Interface OrfFinderInterface - finds every open reading frame across all six reading frames (three
forward, three reverse) of a DNA sequence.
- ProteinPropertiesInterface
- Interface ProteinPropertiesInterface
- SkewCalculatorInterface
- Interface SkewCalculatorInterface