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:

• N Terminal Sequence: The sequence to use at the N-terminal part of the fusion protein.
• C Terminal Sequence: The sequence to use at the C-terminal part of the fusion protein.
• C Terminal Selections (optional): Selection of the C-terminal sequence.
• N Terminal Selections (optional): Selection of the N-terminal sequence.

Input Parameters:

• Linker Sequence (optional): String of the protein sequence to link the two sequences.

Output:

• Fusion Protein: Generated fusion protein sequence as fasta file.
• Selections: Merged selections of the C-terminal and N-terminal sequence, mapped to the new sequence coordinates inside the fusion protein.

Mutate Protein

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

Input: Loaded protein sequence as fasta file.

Input Parameters:

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

Output: Mutated protein sequence as fasta file.

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: Nucleic Acid (DNA) sequence.

Output: 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:

• Protein sequence to translate to DNA: Protein sequence as loaded fasta file.
• Protein selections (optional): Selection of the protein sequence.

Input Parameters:

• Codon Table: Selected from the drop-down menu.

Output: Translated DNA sequence as fasta file.

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:

• Nucleic acid sequence to translate to Protein: DNA sequence as loaded fasta file.
• Nucleic acid selections (optional): Selection of the DNA sequence.

Input Parameters:

• Codon Table: Selected from the drop-down menu.

Output: Translated protein sequence as fasta file.