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Sequence

Fuse Protein

Creates a fusion protein sequence using two protein sequences along with an optional linker sequence. The C-terminal sequence is the last part of the protein to be synthesized, while the N-terminal sequence is synthesized first.

A fusion protein is a protein made by joining protein sequences that were originally part of separate proteins. This can be useful for studying the effects of different domains, give proteins new functions, add binding affinity conferring domains, etc. The general architecture of a fusion protein is one part of a protein sequence added to another one with an optional flexible linker sequence joining the two protein sequences.

Input:

  • Name: Name of the fusion potein.
  • N Terminal Sequence: Loaded fasta file containing the sequence to use as the N-terminal part of the fusion protein. The fasta file must have only a single entry.
  • C Terminal Sequence: Loaded fasta file containing the sequence to use as the C-terminal part of the fusion protein. The fasta file must have only a single entry.
  • C Terminal Selections (optional): Selections of the C-terminal protein sequence.
  • N Terminal Selections (optional): Selections of the N-terminal protein sequence.

Input Parameters:

  • Linker Sequence (optional): The amino acid sequence (as text) to use as the linker between the domains.

Output:

  • Fusion Protein: Generated fusion protein sequence as fasta file.
  • Merged Selections: Original selections that were merged and remapped to the correct amino acids in the fusion protein.

Mutate Protein

Adds a point mutation of a specified amino acid at a specified location of a protein sequence.

Input:

  • Protein Sequence: Fasta file containing the protein sequence to add a mutation to. The fasta file must have only a single protein sequence entry.

Input Parameters:

  • Mutation Position: Position of the amino acid to mutate.
  • Mutation Amino Acid: Select amino acid to mutate the position to from drop-down menu.

Output: Mutated Protein Sequence with the specified mutation in fasta format.

Reverse Complement

Creates the reverse complement of a gene sequence. This is useful for getting the correct forward protein coding DNA sequence when a gene is given on the reverse strand, which can occur with DNA sequences exported from GenBank files.

Input: - Single Sequence Fasta: Fasta file containing the sequence to compute the reverse complement of. The fasta file must have only a single DNA sequence entry.

Output:

  • Generated Sequence: Generated reverse complement of the input sequence as fasta file.

Translate To DNA

Translates a protein sequence to a DNA sequence based upon a given codon table.

A codon table contains information about which DNA base triplets correspond to which amino acid, a property that is different between certain groups of organisms.

Note: The node does currently not support codon optimization. The picked codon per amino acid is always the first occurring one in the codon table. Codon optimization is the process of altering codons to fit certain constraints, such as GC content, avoidance of restriction sites, and more, while not altering the protein sequence the DNA codes for.

The following codon tables are available:

  • Standard (SGC0): The standard code. This is the default value and is used for most organisms, including vertebrate nuclear DNA, invertebrates, plants, and fungi. Examples: Homo sapiens, Arabidopsis thaliana
  • Vertebrate mitochondrial (SGC1): This is used for mitochondrial DNA of vertebrates. Examples: Homo sapiens mitochondria, Mus musculus mitochondria
  • Yeast mitochondrial (SGC2): codon table for mitochondrial DNA of yeast. Examples: Saccharomyces cerevisiae mitochondria.Yarrowia lipolytica mitochondria
  • Mold mitochondrial; Protozoan mitochondrial; Coelenterate mitochondrial; Mycoplasma; Spiroplasma (SGC3): codon table for mitochondrial DNA in mold, protozoans, coelenterate, as well as DNA of mycoplasma and spiroplasma. Example: Plasmodium falciparum mitochondria
  • Invertebrate mitochondrial (SGC4): codon table for mitochondrial DNA of invertebrates. Example: Drosophila melanogaster mitochondria
  • Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear (SGC5): The codon table for the nuclear DNA of ciliates, dasycladaceans and hexamita. Examples: Paramecium tetraurelia, Tetrahymena thermophila
  • Echinoderm mitochondrial; Flatworm mitochondrial (SGC8): The codon table for mitochondrial DNA of echinoderms and flatworms. Example: Schistosoma mansoni
  • Euplotid Nuclear (SGC9): Codon table of euplotid nuclear DNA Example: Euplotes crassus
  • Bacterial, Archaeal and Plant Plastid: This codon table is used for bacterial, archeal and plastid DNA. Examples: Bacillus subtilis, Methanocaldococcus jannaschii
  • Alternative Yeast Nuclear: Used in certain Yeast species such as Candida albicans. Not used in Saccharomyces cerevisiae or Yarrowia lipolytica
  • Ascidian Mitochondrial: Used for mitochondrial DNA of ascidians. Example: Halocynthia roretzi
  • Alternative Flatworm Mitochondrial: Used for some species for flatworm mitochondrial DNA. Example: Radopholus similis
  • Blepharisma Nuclear: This codon table is used for protists of the genus Blepharisma. Example: Blepharisma hyalinum

Input:

  • Single Protein Sequence: Fasta file containing the protein to translate to a nucleic acid sequence. The fasta file must have only a single protein sequence entry.
  • Protein Selections (optional): The selections of the protein sequence. These selections will be converted to fit the converted nucleic acid sequence. Selections can be added through the Add Selection node.

Input Parameters:

  • Codon Table: Select the codon table to use for translation from the drop-down menu.

Output:

  • Translated Sequence: The nucleic acid sequence into which the protein was translated.
  • Selections: Selections of the input sequence adjusted to fit the nucleic acid sequence, if a selection was provided.

Translate To Protein

Translates a DNA sequence into a protein sequence based on a given codon table (see Translate To DNA node for available codon tables).

Input:

  • Single Sequence Fasta: Fasta file containing the nucleic acid to translate to a protein sequence. The fasta file must have only a single DNA sequence entry.
  • Nucleic Acid Selections (optional): The selections of the nucleic acid sequence. These selections will be converted to fit the converted protein sequence. Selections can be added through the Add Selection node.

Input Parameters: - Codon Table: Select the codon table to use for translation from the drop-down menu.

Output:

  • Translated Protein: The protein sequence into which the nucleic acid was translated.
  • Selections: Selections of the input sequence adjusted to fit the protein sequence, if a selection was provided.