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protein sequence database

by Robbie Fisher Published 3 years ago Updated 2 years ago

The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.

Which is a major protein sequence database?

Among all protein sequence databases, UniProt (UniProt Consortium, 2011) is the most widely used one. It provides more annotations than any other sequence database with a minimal level of redundancy through human input or integration with other databases.

What is protein sequence in bioinformatics?

Protein Sequence Analysis is the process of subjecting a protein or peptide sequence to one of a wide range of analytical methods to study its features, function, structure, or evolution. Methodologies used include sequence alignment, searches against biological databases, and other methods.

What is SWISS-PROT protein sequence database?

SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases.

Is GenBank a protein sequence database?

The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations....GenBank.ContentPrimary citationPMID 21071399Release date1982AccessData formatXML ASN.1 Genbank format13 more rows

What is protein sequencing used for?

Protein sequencing is used to identify the amino acid sequence and its conformation. The identification of the structure and function of proteins is important to understand cellular processes.

Which of the following is protein database?

SWISS-PROT is a primary database of protein sequences. It provides all information about a specific protein sequence, structure, and function with its post-translational modifications.

Is SWISS-PROT and UniProt same?

Swiss-Prot (created in 1986) is a high quality manually annotated and non-redundant protein sequence database, which brings together experimental results, computed features and scientific conclusions. UniProtKB/Swiss-Prot is now the reviewed section of the UniProt Knowledgebase.

What does SWISS-PROT entry contain?

Each entry in SWISS-PROT contains the following information: Known protein sequences, references, taxonomic information, annotations, etc. The protein entry contains a total of 14 topics. You can use this database to query some information you need: Query for aliases of target proteins.

Is SWISS-PROT a secondary database?

Complete answer: SWISS PROT is a protein sequence database. Annotations in the database provide all the information regarding the structure and function of a particular protein along with its functions and modifications if any. The data is all primary and easily accessible.

What type of database is GenBank?

GenBank® is a comprehensive database that contains publicly available nucleotide sequences for more than 300 000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun ( ...

What type of database is NCBI?

The NCBI taxonomy database is a central organizing principle for the Entrez biological databases and provides links to all data for each taxonomic node, from superkingdoms to subspecies (9). The taxonomy database reflects sequence data from almost 260 000 formally described species.

What is SRA database?

The Sequence Read Archive (SRA, previously known as the Short Read Archive) is a bioinformatics database that provides a public repository for DNA sequencing data, especially the "short reads" generated by high-throughput sequencing, which are typically less than 1,000 base pairs in length.

What are protein sequence databases?

A variety of protein sequence databases exist, ranging from simple sequence repositories, which store data with little or no manual intervention in the creation of the records, to expertly curated universal databases that cover all species and in which the original sequence data are enhanced by the manual addition of further information in each sequence record. As the focus of researchers moves from the genome to the proteins encoded by it, these databases will play an even more important role as central comprehensive resources of protein information. Several the leading protein sequence databases are discussed here, with special emphasis on the databases now provided by the Universal Protein Knowledgebase (UniProt) consortium.

What is a Uniparc database?

UniParc is the most comprehensive publicly accessible non-redundant protein sequence collection available . It contains publicly available protein sequences from Swiss-Prot, TrEMBL, PIR-PSD, EMBL, Ensembl [31], International Protein Index (IPI) ( http://www.ebi.ac.uk/IPI ), PDB, RefSeq, FlyBase, WormBase [32] and the patent offices in Europe, the United States and Japan, making it the most comprehensive protein sequence database available. While a protein sequence may exist in multiple databases and more than once in a given database, UniParc stores every unique sequence only once and assigns a unique UniParc identifier. Furthermore, UniParc provides cross-references to the source databases (accession numbers), sequence versions, and status (active or obsolete). A UniParc sequence version is also provided, and incremented each time the underlying sequence changes, thus making it possible to observe sequence changes in all source databases.

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