Bioinformatics Tools and Concepts

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Questions and Answers

What is the main advantage of using BLOSUM for comparing sequences?

  • It is better suited for comparing distantly related sequences (correct)
  • It is faster than other algorithms
  • It is more sensitive to sequence divergence
  • It has a higher accuracy rate

Which type of BLAST algorithm is specifically designed for searching short similar sequences?

  • blastx
  • tblastn
  • blastn (correct)
  • megablast

What feature of a gene does an exon represent?

  • The part that is protein coding (correct)
  • The overall length of the gene
  • The untranslated regulatory region at the gene ends
  • The initial seed for cross-species comparisons

What does a heuristic algorithm do in the context of solving a problem?

<p>Limits the search space and time without finding the optimal solution (D)</p>
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Which BLAST program is best suited for closely related sequences with a target percent identity of 95% or more?

<p>megablast (B)</p>
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What is the main difference between blastn and tblastx algorithms?

<p>The direction of sequence translation (D)</p>
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What does the term Megablast refer to in the context of the provided text?

<p>Megablast is a program for analyzing short similar sequences. (B)</p>
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What is the main difference between BLOSUM and PAM matrices?

<p>BLOSUM matrices are used for closely related sequences, while PAM matrices are for distantly related species. (B)</p>
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What is the significance of having a lower N50 value when analyzing sequences?

<p>Lower N50 values imply fewer gaps and higher confidence in the sequence. (D)</p>
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What is a Contig in the context of genetic sequencing?

<p>A Contig represents a larger portion of a read with some gaps. (A)</p>
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In what way does the Blossom algorithm differ from the Pam matrix?

<p>Blossom focuses on observed substitutions, while Pam focuses on mutation rates. (B)</p>
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When choosing between Blastn, Blastp, and Blastx programs, which would be most suitable for short dissimilar sequences?

<p>Blastp (C)</p>
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