Mutalyzer
Encyclopedia
Mutalyzer is a tool which was primarily developed to check the description of sequence variants
identified in a gene
during genetic testing
. Mutalyzer applies the rules of the standard human sequence variant nomenclature and can correct descriptions accordingly. Apart from the sequence variant description, Mutalyzer requires a DNA sequence
record containing the transcript and protein
feature annotation as a reference. Mutalyzer 2 accepts GenBank
and Locus Reference Genomic
(LRG) records. The annotation is also used to apply the correct codon translation
tables and generate DNA and protein variant descriptions for any organism.
is generally performed in families with hereditary disease. Any sequence variant identified in a gene can be described in test reports using the position of the change and the nucleotide
or amino acid
involved. With this simple rule, a deletion of the nucleotide guanine
(G) in a stretch of 4 G nucleotides might be described in 4 different ways, when each of the G positions is used. Although different descriptions do not affect the functional consequences of the change, they may obfuscate the fact that two persons share the same variant or the real frequency of a variant in the population. The standard human sequence variant nomenclature proposed by the Human Genome Variation Society was developed to solve this problem. Proper variant descriptions are expected to facilitate searches for more information about the functional consequences in the literature and in locus-specific mutation databases.
Mutalyzer is used by the Leiden Open Variation Database (LOVD), which stores sequence variant information for many human genes, to check variant descriptions before submission of new data. This helps data sharing, display and integration with other genetic resources (e.g., Ensembl
, UCSC Genome Browser
, NCBI sequence viewer)
Mutation
In molecular biology and genetics, mutations are changes in a genomic sequence: the DNA sequence of a cell's genome or the DNA or RNA sequence of a virus. They can be defined as sudden and spontaneous changes in the cell. Mutations are caused by radiation, viruses, transposons and mutagenic...
identified in a gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
during genetic testing
Genetic testing
Genetic testing is among the newest and most sophisticated of techniques used to test for genetic disorders which involves direct examination of the DNA molecule itself. Other genetic tests include biochemical tests for such gene products as enzymes and other proteins and for microscopic...
. Mutalyzer applies the rules of the standard human sequence variant nomenclature and can correct descriptions accordingly. Apart from the sequence variant description, Mutalyzer requires a DNA sequence
DNA sequence
The sequence or primary structure of a nucleic acid is the composition of atoms that make up the nucleic acid and the chemical bonds that bond those atoms. Because nucleic acids, such as DNA and RNA, are unbranched polymers, this specification is equivalent to specifying the sequence of...
record containing the transcript and protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
feature annotation as a reference. Mutalyzer 2 accepts GenBank
GenBank
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced and maintained by the National Center for Biotechnology Information as part of the International Nucleotide Sequence...
and Locus Reference Genomic
Locus Reference Genomic
Locus Reference Genomic is a DNA sequence format that was developed to aid in curating locus specific databases that record DNA sequence variation which can result in inherited diseases. LRGs have fixed sequences that are independent of the genome so that they provide a stable framework for...
(LRG) records. The annotation is also used to apply the correct codon translation
Genetic code
The genetic code is the set of rules by which information encoded in genetic material is translated into proteins by living cells....
tables and generate DNA and protein variant descriptions for any organism.
Background
Genetic testingGenetic testing
Genetic testing is among the newest and most sophisticated of techniques used to test for genetic disorders which involves direct examination of the DNA molecule itself. Other genetic tests include biochemical tests for such gene products as enzymes and other proteins and for microscopic...
is generally performed in families with hereditary disease. Any sequence variant identified in a gene can be described in test reports using the position of the change and the nucleotide
Nucleobase
Nucleobases are a group of nitrogen-based molecules that are required to form nucleotides, the basic building blocks of DNA and RNA. Nucleobases provide the molecular structure necessary for the hydrogen bonding of complementary DNA and RNA strands, and are key components in the formation of stable...
or amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
involved. With this simple rule, a deletion of the nucleotide guanine
Guanine
Guanine is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine . In DNA, guanine is paired with cytosine. With the formula C5H5N5O, guanine is a derivative of purine, consisting of a fused pyrimidine-imidazole ring system with...
(G) in a stretch of 4 G nucleotides might be described in 4 different ways, when each of the G positions is used. Although different descriptions do not affect the functional consequences of the change, they may obfuscate the fact that two persons share the same variant or the real frequency of a variant in the population. The standard human sequence variant nomenclature proposed by the Human Genome Variation Society was developed to solve this problem. Proper variant descriptions are expected to facilitate searches for more information about the functional consequences in the literature and in locus-specific mutation databases.
Mutalyzer is used by the Leiden Open Variation Database (LOVD), which stores sequence variant information for many human genes, to check variant descriptions before submission of new data. This helps data sharing, display and integration with other genetic resources (e.g., Ensembl
Ensembl
Ensembl is a joint scientific project between the European Bioinformatics Institute and the Wellcome Trust Sanger Institute, which was launched in 1999 in response to the imminent completion of the Human Genome Project...
, UCSC Genome Browser
UCSC Genome Browser
The University of California, Santa Cruz is an up-to-date source for genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations...
, NCBI sequence viewer)