Receiving Helpdesk

uniprot blast

by Danielle Kerluke Published 3 years ago Updated 2 years ago

Is the UniProt BLAST service still available?

This BLAST service was shut down in March 2022. You can find most of the protein databases that were available here at the UniProt BLAST service . For nucleotide databases we recommend that you use the EBI BLAST service or the NCBI BLAST service .

What is blast?

BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. Learn more The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.

What is UniProt?

The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. Manually annotated and reviewed.

Where can I perform a BLAST sequence similarity search?

BLAST sequence similarity search against UniProtKB or taxonomic subdivisions, complete proteomes, UniRef, PDB or UniParc - on the UniProt web site.

What is UniProt Blast?

Last modified November 22, 2021. The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation.

What is UniProt used for?

UniProt is the central resource for storing and interconnecting information from large and disparate sources, and the most comprehensive catalog of protein sequence and functional annotation.

How do I run a Blast in UniProt?

Select the Blast tab of the toolbar to run a sequence similarity search with the BLAST (Basic Local Alignment Search Tool) program:Enter either a protein or nucleotide sequence (raw sequence or fasta format) or a UniProt identifier into the form field.Click the Blast button.

What is the difference between UniProt and Swiss-Prot?

Protein families and groups of proteins are continuously reviewed to keep up with current scientific findings. UniProtKB/TrEMBL is a computer-annotated (unreviewed) supplement to Swiss-Prot, which strives to gather all protein sequences that are not yet represented in Swiss-Prot.

What are the features of UniProt?

THE UNIPROT KNOWLEDGEBASE (UNIPROT)High-quality annotation. ... Manual annotation by curators based on literature and sequence analysis. ... Automatic classification and annotation. ... High-quality Automated and Manual Annotation of microbial Proteomes (HAMAP) ... Standardized nomenclature and controlled vocabularies.More items...

Who created Swiss-Prot?

SWISS-PROT (1) is an annotated protein sequence database, which was created at the Department of Medical Biochemistry of the University of Geneva and has been a collaborative effort of the Department and the European Molecular Biology Laboratory (EMBL), since 1987.

What is a good Bitscore?

The bit-score provides a better rule-of-thumb for inferring homology. For average length proteins, a bit score of 50 is almost always significant. A bit score of 40 is only significant (E() < 0.001) in searches of protein databases with fewer than 7000 entries.

How do you use BLAST?

0:051:54How to Use NCBI Blast - YouTubeYouTubeStart of suggested clipEnd of suggested clipInformation. Website by clicking on blast in the popular. Resources menu. Step 2 choose a blastMoreInformation. Website by clicking on blast in the popular. Resources menu. Step 2 choose a blast program to run from the basic blast menu.

How many sequences are in UniProt?

UniProt release 2020_04 contains over 189 million sequence records (Figure 1), with >292 000 proteomes, the complete set of proteins believed to be expressed by an organism, originating from completely sequenced viral, bacterial, archaeal and eukaryotic genomes available through the UniProtKB Proteomes portal (https:// ...

Is UniProt a secondary database?

Hybrid databases and families of databases Many data resources have both primary and secondary characteristics. For example, UniProt accepts primary sequences derived from peptide sequencing experiments.

Who maintains Swiss-Prot?

1. Swiss-Prot and TrEMBL. SWISS-PROT is a protein sequence database containing detailed annotations. It was established in 1986 and jointly maintained by the department of medical biochemistry of the University of Geneva and the EMBL data library (now EBI) since 1987.

What is a UniProt number?

Last modified April 10, 2018. The proteome identifier (UPID) is the unique identifier assigned to the set of proteins that constitute the proteome. It consists of the characters 'UP' followed by 9 digits, is stable across releases and can therefore be used to cite a UniProt proteome.

Filters and views

You can use filters on the left hand side to narrow down your search results, e.g. to limit the results to a particular species. You can also map the results to UniProt protein databases UniProtKB, UniRef and UniParc. You can view results by taxonomy or in plain text format.

Alignments table

More detail about each result can be seen in the ‘Alignments’ table under the ‘Overview’ section, showing the query sequence aligned to each subject sequence.

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