8 Questions
What does BLASTx stand for?
Basic Local Alignment Search Tool, translated in X language
What is the main function of BLASTx?
Translates the query nucleotide sequence into all six possible reading frames and compares the translations against the protein sequence database
What is GenBank?
A comprehensive, open-access database of publicly available nucleotide sequences
Who maintains GenBank?
The National Center for Biotechnology Information (NCBI), a part of the National Library of Medicine (NLM) at the National Institutes of Health (NIH)
What is the purpose of using BLASTx to search GenBank?
To compare the query sequence against the vast collection of annotated sequences in GenBank
What does BLASTx do to the query sequence before comparing it to GenBank?
Translates the query nucleotide sequence into all six possible reading frames
What information is provided in the results of a BLASTx search against GenBank?
Information on the similarity between the query sequence and known protein sequences in GenBank, including functional annotations and putative identities
Who submits the data to GenBank?
Researchers
Study Notes
BLASTx
- BLASTx stands for Basic Local Alignment Search Tool, translated in X language
- A variant of the BLAST algorithm used for comparing a query protein sequence against a protein sequence database
- Translates the query nucleotide sequence into all six possible reading frames and compares the translations against the protein sequence database
- Useful for identifying the presence of a protein-coding region in a nucleotide sequence
NCBI GenBank
- GenBank is a comprehensive, open-access database of publicly available nucleotide sequences
- Maintained by the National Center for Biotechnology Information (NCBI), a part of the National Library of Medicine (NLM) at the National Institutes of Health (NIH)
- Contains annotated sequences for a wide range of organisms, including genomes, genes, proteins, and transcripts
- Data are submitted by researchers, annotated by NCBI staff, and made available to the public
BLASTx and GenBank Integration
- BLASTx can be used to search GenBank, allowing users to compare their query sequence against the vast collection of annotated sequences in GenBank
- Users can submit a nucleotide sequence and BLASTx will translate it and compare it against the protein sequences in GenBank
- Results provide information on the similarity between the query sequence and known protein sequences in GenBank, including functional annotations and putative identities
Test your knowledge on how to use BLASTx to search GenBank and compare query sequences against annotated sequences. Learn about the integration of these two powerful bioinformatics tools. Identify protein-coding regions and get functional annotations.
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