8 Questions
Explain the purpose of BLAST and how it is used in bioinformatics research.
BLAST (Basic Local Alignment Search Tool) is used to compare biological sequences to determine similarity and identify functional and evolutionary relationships. It is used in bioinformatics research to find matches between a query sequence and a database of sequences, helping to infer the function of the query sequence and its evolutionary history.
What is an Open Reading Frame (ORF) and how is it different from a Coding Sequence (CDS)?
An Open Reading Frame (ORF) is a sequence of DNA that could potentially encode a protein. It starts with a start codon (usually ATG) and ends with a stop codon (e.g., TAA, TAG, or TGA). A Coding Sequence (CDS) is the actual region of DNA that is translated to make proteins. An ORF may contain introns, while a CDS is the mature mRNA sequence that is translated into a protein.
Describe the potential functions encoded by the practice ORF finder output 'Var1 = rps3 (ribosomal protein S3) ONE ORF but two functions are encoded. Ribosomal protein and Endonuclease activity (fusion ORF or hybrid ORF or fused gene).'
The output suggests that the sequence encodes a single Open Reading Frame (ORF) that has two distinct functions: ribosomal protein S3 and endonuclease activity. This type of ORF is called a fusion ORF, hybrid ORF, or fused gene, indicating that it combines the functions of two separate genes or protein domains.
What are the key features that computer algorithms look for when searching for Open Reading Frames (ORFs) in DNA sequences?
Computer algorithms search for start and stop codons (e.g., ATG for start and TAA, TAG, or TGA for stop), as well as potential ribosome binding sites (Shine-Dalgarno sequences). These features help identify potential ORFs that could encode proteins within a given DNA sequence.
Explain the purpose of using BLAST and list at least three applications of BLAST in molecular microbiology research.
BLAST is used to compare a query sequence with sequences in a database to determine homologs, paralogs, identify a species, discover a new gene, and determine gene variants.
Describe the steps involved in using BLAST for sequence comparison and specify the significance of selecting a database and setting algorithm parameters.
The steps involved in using BLAST for sequence comparison include selecting a BLAST program, inputting the query sequence, selecting a database (such as the nr database), setting algorithm parameters, and setting the scoring matrix. Selecting the database and setting algorithm parameters are significant for refining the search and obtaining accurate results.
Explain the principle behind BLAST and how it aids in searching through a database for sequence matches.
The principle behind BLAST involves breaking down the query sequence into a library of short sequences, making it easier to find short matches. These short sequences are then used to search through a database, aiding in the identification of sequence matches.
Using Saccharomyces cerevisiae's mitochondrial genome with accession number MW122508.1 as an example, describe how one can explore GenBank using BLAST.
One can explore GenBank using BLAST by inputting the accession number MW122508.1 as the query sequence, selecting the appropriate BLAST program, choosing the nr database, and setting algorithm parameters as needed to search for homologous sequences.
Test your knowledge of computational molecular microbiology with this quiz covering sequence databases, sequence comparison, BLAST, and exploring specific genomes in NCBI GenBank.
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