Sequence Comparison in Computational Molecular Microbiology

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.

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.

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.

<p>More information on the differences between global and local alignment can be found at <a href="https://www.majordifferences.com/2016/05/difference-between-global-and-local">https://www.majordifferences.com/2016/05/difference-between-global-and-local</a>.</p> Signup and view all the answers

<p>Global alignment and local alignment</p> Signup and view all the answers

<p>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</p> Signup and view all the answers

<p>3 for protein and 11 for DNA</p> Signup and view all the answers

<p>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</p> Signup and view all the answers

<p>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.</p> Signup and view all the answers

<p>Dayhoff’s PAM (Accepted Point Mutation) matrix and Henikoffs’s BLOSUM (BLOck SUbstitution Matrix) matrix</p> Signup and view all the answers

<p><a href="https://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm">https://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm</a>, <a href="https://www.ncbi.nlm.nih.gov/books/NBK62051/">https://www.ncbi.nlm.nih.gov/books/NBK62051/</a>, <a href="http://upload.wikimedia.org/wikipedia/en/5/56/Query_word.jpg">http://upload.wikimedia.org/wikipedia/en/5/56/Query_word.jpg</a></p> Signup and view all the answers

<p>Pevzner J. 2015. Bioinformatic and Functional Genomics</p> Signup and view all the answers