blastx
BLAST Search for DNA Query in Protein Database
The question asks to identify the BLAST program suitable for searching a genomic DNA sequence against a protein sequence database to find homologous sequences.
BLAST Program Functions
BLAST (Basic Local Alignment Search Tool) offers several programs optimized for different query and database types. Understanding these distinctions is key:
- blastp: Compares a protein query against a protein sequence database.
- blastn: Compares a nucleotide query against a nucleotide sequence database.
- blastx: Compares a nucleotide query (translated into protein) against a protein sequence database.
- tblastn: Compares a protein query against a nucleotide sequence database (which is translated into protein).
Selecting the Right BLAST Program
To search a genomic DNA query within a protein sequence database, the DNA query must first be translated into possible protein sequences. The blastx program is designed for this purpose. It takes the nucleotide query, translates it conceptually across all possible reading frames, and then searches these translated protein sequences against the provided protein database.
Therefore, when using a genomic DNA sequence as the query and searching against a protein database, blastx is the appropriate tool.
| Program | Query Type | Database Type | Purpose |
|---|---|---|---|
| blastp | Protein | Protein | Protein vs. Protein search |
| blastn | Nucleotide | Nucleotide | Nucleotide vs. Nucleotide search |
| blastx | Nucleotide (Translated) | Protein | DNA query vs. Protein database |
| tblastn | Protein | Nucleotide (Translated) | Protein vs. DNA (translated) search |
Conclusion
Based on the function of translating a nucleotide query into protein sequences before searching a protein database, blastx is the correct program for this specific task.
Important Questions from Methods in Microbiology
- Which one of the following programs is used for finding distantly related (or remote) protein homologs?
- Which one of the following is used for global alignment of two protein sequences?
- Correctly match the following Bioinformatic tool/Database with its respective Utility.
Bioinformatic tool/Database Utility P. BLAST 1. Database for 3D protein structures Q. Bowtie 2. Tool to identify similarity of a query sequence to existing sequences available in databanks R. AlphaFold 3. Tool to align short read DNA sequences obtained from Next-generation sequencing to a reference genome S. PDB 4. AI tool to predict protein structures - Which of the following is NOT used for generating an optimal alignment of two nucleotide sequences?
Consider the following alignment of two DNA sequences:
AGTAAC
AA--AC
Assuming an affine gap scoring scheme of an identity matrix for substitution, a gap initiation penalty of 1 and a gap extension penalty of 0.1, the score of the alignment is (up to one decimal place)_______.
