12 Questions
How do you compare sequences?
Sequences can be compared by using methods such as pairwise alignment and multiple sequence alignment. These methods help identify similarities and differences between sequences by considering factors like gaps, substitutions, and recombination.
What are the major components of sequence alignment?
The major components of sequence alignment include: 1. Type of the alignment in consideration 2. Scoring system (e.g., substitution matrix) to rank alignments 3. Algorithm to find the optimal alignment 4. Statistical method to assess the significance of the alignment.
What are the differences between local and global alignment?
Local alignment prioritizes highest similarity matches, aligns substrings, and is suitable for database search or conserved domain search. Global alignment aligns the whole string with an end-to-end alignment approach, and is good for aligning closely related sequences with similar length.
Where can one find more information on the differences between global and local alignment?
More information on the differences between global and local alignment can be found at https://www.majordifferences.com/2016/05/difference-between-global-and-local.
What are the two types of alignment algorithms mentioned in the text?
Global alignment and local alignment
What are some examples of substitution matrices mentioned in the text?
Jukes and Cantor model (JC), Kimura model (K2P or K3P), Dayhoff’s PAM (Accepted Point Mutation) matrix, and Henikoffs’s BLOSUM (BLOck SUbstitution Matrix) matrix
What is the default word size for protein and DNA in the BLAST algorithm?
3 for protein and 11 for DNA
What is the purpose of the BLAST algorithm?
To generate local alignments, developed for database search, and to make a list of all 'neighboring words' of a fixed length and search in the database and further extend in both directions
Based on biological significance, what do BLOSUM matrices include?
They include the fact that some amino acids show up in blocks (bias) – regions in related proteins may contain aromatic amino acids, acidic or basic, polar and/or nonpolar amino acids, etc.
What are some examples of amino-acid substitution matrices?
Dayhoff’s PAM (Accepted Point Mutation) matrix and Henikoffs’s BLOSUM (BLOck SUbstitution Matrix) matrix
What are the links to additional resources mentioned in the text?
What are the two books mentioned in the text as references?
Pevzner J. 2015. Bioinformatic and Functional Genomics
Test your knowledge of sequence comparison, pairwise alignment, multiple sequence alignment, and phylogenetic tree construction in computational molecular microbiology. This quiz covers concepts such as sequence databases, differences between comparing sequences, and factors to consider during sequence alignment.
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