Computational Molecular Microbiology: Sequence Alignment Practice

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Questions and Answers

What are the methods for multiple sequence alignment (MSA)?

The methods for multiple sequence alignment include exact method, progressive alignment method (e.g., ClustalW), iterative refinement method (e.g., PRALINE, MUSCLE, T-COFFEE), consistency-based method (e.g., MAFFT), homology-based method (e.g., MAFFT), and structure-based method (e.g., Expresso).

What is the purpose of a guide tree in multiple sequence alignment (MSA)?

The guide tree helps in MSA by showing that sequences are related by a phylogenetic tree, and it also helps in position-specific scoring, where some positions are more conserved than others.

What is the Progressive alignment method in MSA?

The Progressive alignment method is a type of MSA method where sequences are aligned step by step, with the most similar sequences being aligned first and then the alignment is progressively refined.

How does the probability of a multiple alignment relate to the correct phylogenetic tree for the sequences?

Given the correct phylogenetic tree for the sequences, the probability of a multiple alignment is the product of the probabilities of all the evolutionary events necessary to produce that alignment. Signup and view all the answers

In what context is MSA (multiple sequence alignment) used in bioinformatics?

MSA is used in bioinformatics for applications such as building databases, finding conserved domains, analyzing genomes, studying mutation and molecular evolution, and generating phylogenetic trees. Signup and view all the answers

What are some databases and tools used for finding conserved domains in MSA applications?

Some databases and tools used for finding conserved domains in MSA applications include protein classification databases like Pfam, SMART, and InterPro, as well as the Conserved Domain Database (CDD) and WebLogo program. Signup and view all the answers

What is the purpose of PRALINE in the context of MSA?

PRALINE is a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information, and it is used to create alignments focusing on specific conserved motifs of proteins. Signup and view all the answers

What are PSI-BLAST and PHI-BLAST used for in bioinformatics?

PSI-BLAST is used for finding distantly related proteins that match a protein of interest, utilizing the MSA strategy to create a profile for iterative search. PHI-BLAST is used to search a database with a short query corresponding to a pattern, such as specific amino acid patterns in protein families. Signup and view all the answers

What does the process of generating a phylogenetic tree require?

The process of generating a phylogenetic tree requires multiple sequence alignment (MSA) to align and compare the evolutionary relationships of sequences and accession numbers of the organisms of interest. Signup and view all the answers

What are some examples of accession numbers used for phylogenetic tree building in the provided text?

Some examples of accession numbers used for phylogenetic tree building in the provided text include NP_000198.1 (human), NP_001008996.1 (chimpanzee), NP_062003.1 (rat), NP_001123565.1 (dog), NP_001172013.1 (mouse), NP_001075804.1 (rabbit), NP_001103242.1 (pig), NP_990553.1 (chicken), NP_001172055.1 (cow), P01318.2 (sheep), XP_003422420.1 (elephant), and P67974.1 (sperm whale). Signup and view all the answers

What is the purpose of the scale and color code used in the PRALINE PSI P450 alignment visualization?

The scale and color code in the PRALINE PSI P450 alignment visualization represent the conservation level of amino acids, with blue indicating less conservation and red indicating high conservation. The scale ranges from 0 to 9, and the color coding helps in visualizing the conservation patterns across sequences. Signup and view all the answers

Why is PHI-BLAST preferable for searching a database with a short query corresponding to a pattern?

PHI-BLAST is preferable for searching a database with a short query corresponding to a pattern because it is designed to identify specific patterns or motifs within protein sequences, making it suitable for searching for conserved regions or specific amino acid patterns in protein families. Signup and view all the answers

Study Notes

Methods for Multiple Sequence Alignment (MSA)

MSA techniques include progressive alignment, iterative methods, and consistency-based approaches.
Each method aims to align multiple sequences to identify similarities and differences effectively.

Purpose of a Guide Tree in MSA

A guide tree represents the evolutionary relationships between sequences, helping to inform the order of alignment.
It facilitates progressive alignment by providing a hierarchical structure for aligning sequences based on their similarity.

Progressive Alignment Method in MSA

This method involves aligning the most similar sequences first, gradually adding less similar sequences based on the guide tree.
Progressive alignment is efficient but can be sensitive to errors in early alignments.

Probability of Multiple Alignment and Phylogenetic Trees

The probability of obtaining a particular multiple alignment is linked to the likelihood of the correct phylogenetic tree that governs the sequences' evolution.
A higher probability of alignment often indicates a more accurate representation of evolutionary relationships.

Context of MSA in Bioinformatics

MSA is widely used for identifying conserved regions, studying evolutionary relationships, and predicting structural or functional information of proteins and genes.
It is crucial in comparative genomics and protein function prediction.

Databases and Tools for Conserved Domains in MSA

Common databases include Pfam, SMART, and CDD for finding conserved domains in sequences.
Tools like HMMER and InterProScan assist in identifying functional domains within multiple sequence alignments.

Purpose of PRALINE in MSA

PRALINE is a web-based tool designed for performing multiple sequence alignment with an emphasis on incorporating secondary structure information.
It aims to improve alignment accuracy by considering both sequence and structural data.

Use of PSI-BLAST and PHI-BLAST in Bioinformatics

PSI-BLAST is used for sensitive sequence similarity searching and identifies homologous sequences iteratively to refine alignments.
PHI-BLAST is specifically designed to find motifs; it searches for short sequences that correspond to conserved patterns within a database.

Requirements for Generating a Phylogenetic Tree

Creating a phylogenetic tree requires aligned sequences, a model of sequence evolution, and methods to estimate tree topology.
Additional data, such as bootstrap values, can enhance the robustness of phylogenetic trees.

Examples of Accession Numbers in Phylogenetic Tree Building

Accession numbers like GenBank identifiers serve as unique keys for retrieving specific sequences necessary for phylogenetic analysis.
They facilitate the integration of data from various biological databases.

Purpose of Scale and Color Code in PRALINE PSI P450 Alignment Visualization

The scale and color code in PRALINE visualizations provide visual cues that differentiate conserved regions and highlight important residues in alignments.
This enhances the interpretability of the alignment and aids in the identification of functionally relevant features.

Preference for PHI-BLAST with Short Queries

PHI-BLAST is advantageous when searching for short query sequences corresponding to specific patterns, as it optimizes the search for conserved motifs against large databases.
This specialization improves search efficiency and accuracy for motif-based queries.

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Description

Test your skills in sequence alignment with this practice quiz covering pairwise alignment, multiple sequence alignment, and phylogenetic tree construction. Work with different sequences and practice aligning them accurately.