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The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
Sequence similarity searches / BLAST submissions Overview BLAST (Basic Local Alignment Search Tool) is a widely used algorithm in bioinformatics that identifies regions of similarity between biological sequences (like proteins, DNA, or RNA).
BLAST sequence similarity search against UniProtKB or taxonomic subdivisions, complete proteomes, UniRef, PDB or UniParc - on the UniProt web site.
How to use BLAST Select the 'BLAST' tab of the toolbar at the top of the page to run a sequence similarity search with the BLAST program. Enter either a protein or nucleotide sequence or a UniProt identifier into the form field (Figure 49). You can submit multiple sequences at a time, up to a maximum of 5 sequences, in which case a job will be created in your dashboard for each of the ...
NCBI provides a web interface to run BLAST searches. However, it is also possible to download the databases to search locally. This post shares the process of downloading the BLAST+ suite of command-line tools, setting up the Swiss-Prot database, and performing a simple blastp search. The source code is available
The Swiss-Prot group, co-led by Alan Bridge and Paul Thomas, excels in generating machine-readable knowledge of biology from the ever-growing body of scientific publications. The team harnesses the power of deep learning methods to accelerate literature triage and data extraction, thus delivering the most accurate and comprehensive information to users in a timely manner.
2. Choose Standard protein-protein BLAST [blastp] 3. Select database. Two commonly used databases for protein sequence searching: swissprot - SWISS-PROT is a high quality protein sequence database with excellent annotations. Minimal redundancy but poorer sequence coverage. nr - Non-Redundant database.
SWISS-PROT contains the information about the name and origin of the protein, protein attributes, general information, ontologies, sequence annotation, amino acid sequence, bibliographic references, cross-references with sequence, structure and interaction databases, and entry information. An example for human lysozyme is shown in Figure 1.13.
UniProtKB/Swiss-Prot is a manually annotated, non-redundant protein sequence database. As it is well-annotated and curated, the Swiss-Prot database gives informative results when searched locally using blastp and blastx.
Developed by the Swiss-Prot group and the UniProt Consortium partners at EMBL-EBI and PIR, and supported by the SIB Swiss Institute of Bioinformatics. UniProt is an ELIXIR Core Data Resource and a Global Core Biodata Resource.