NCBI Minute: Five Teaching Examples Using BLAST

Summary

In this webinar, Peter Cooper from the NCBI introduces a series of teaching examples using the BLAST service, aimed at enhancing bioinformatics education. He covers BLAST's functionality for sequence alignment and identification, sharing practical tips on selecting databases, adjusting parameters, and interpreting results. The session demonstrates five key bioinformatics applications, including bacterial identification, primer design, phylogenetic tree generation, and protein domain analysis. Cooper emphasizes the importance of database selection for efficient searches and highlights related tools like MOLE-BLAST and Primer-BLAST. The session concludes with answers to user questions, offering resources for further exploration.

Takeaways

• 😀 The webinar focused on BLAST (Basic Local Alignment Search Tool), a powerful tool for sequence alignment and comparison in bioinformatics.
• 😀 BLAST is commonly used to find homologous sequences in databases, with applications in gene discovery, protein structure, and function analysis.
• 😀 There are different BLAST tools tailored to specific types of queries: Nucleotide BLAST (blastn) for DNA sequences and Protein BLAST (blastp) for protein sequences.
• 😀 BLAST outputs results in multiple formats, including tabular and graphical representations, helping users visualize sequence relationships and alignments.
• 😀 The webinar emphasized the importance of understanding BLAST’s parameters, such as E-value, to optimize search results.
• 😀 It introduced tools like PSI-BLAST and COBALT for more advanced sequence analysis, including iterative searches and alignment using conserved domains.
• 😀 PSI-BLAST helps refine results through multiple iterations, improving the detection of distant homologs by adjusting for sequence divergence.
• 😀 COBALT (Constraint-based Multiple Alignment Tool) generates multiple sequence alignments using protein domain constraints to build a guide tree.
• 😀 The use of conserved domains within proteins is a key feature of COBALT, providing a more accurate alignment compared to traditional methods.
• 😀 Participants were encouraged to explore additional examples from the provided materials and contact Peter Cooper for further questions about the examples.
• 😀 The webinar concluded by providing contact information for inquiries, including Peter Cooper’s email for specific questions and the general webinars address for broader queries.

Q & A

What is BLAST and why is it important in bioinformatics?

BLAST (Basic Local Alignment Search Tool) is a widely used sequence similarity tool that finds high-scoring local alignments between two biological sequences. It helps identify similarities and relationships between sequences, which is key for tasks like gene annotation, homology search, and identifying organisms or proteins.

What does the Expect value in a BLAST search represent?

The Expect value (E-value) represents the number of hits with the same or better score than expected by chance. A lower E-value indicates a more statistically significant result, meaning that the alignment is less likely to be due to random chance.

Why is it important to use a smaller database in a BLAST search?

Using a smaller database in a BLAST search increases the likelihood of obtaining meaningful results and reduces search time. Larger databases result in higher E-values and can lead to false positives, making the search less efficient and harder to interpret.

What is the difference between the different nucleotide search programs in BLAST?

BLAST uses different search programs for nucleotide sequences, such as 'megablast' for highly similar sequences and 'blastn' for more general searches. You can also use 'blastx' for translating nucleotide sequences and comparing them to protein databases.

What is the role of 'Primer BLAST' in bioinformatics?

Primer BLAST helps design primers for PCR (Polymerase Chain Reaction) by checking their specificity against a given database. It ensures that the primers amplify only the desired sequence and do not match non-target sequences in the genome.

How can MOLE-BLAST help in bioinformatics applications?

MOLE-BLAST is a tool that combines the power of BLAST with multiple sequence alignment, allowing users to cluster sequences and generate phylogenetic trees. It's particularly useful for analyzing 16S rRNA sequences and understanding bacterial diversity.

What are the key differences between COBALT and other multiple sequence alignment tools like ClustalW?

COBALT (Constraint-based Multiple Alignment Tool) uses conserved domain matches to generate a guide tree for alignment, ensuring higher accuracy in aligning functionally important regions of proteins. In contrast, ClustalW uses a guide tree based on sequence similarity, which may not always reflect functional relevance.

Why did the lemur not appear in the results during the ape mitochondrial genome search?

The lemur did not appear in the search results because the database was limited to the superfamily Hominoidea (great apes), which excludes the lemur. If the search had been expanded to include all primates, the lemur would have been included.

How does BLAST handle large sequence databases to optimize search results?

BLAST optimizes large sequence databases by offering ways to reduce the search space, such as using organism filters or specific queries. By narrowing the search scope, BLAST can return more relevant and statistically significant results.

What are the benefits of using BLAST for phylogenetic analysis?

BLAST can be used for phylogenetic analysis by identifying sequence relationships and generating phylogenetic trees. The alignment results help visualize evolutionary relationships, such as those between different ape species or paralogous genes.