Name : Divya Aggarwal

Exam Roll no. : 21428BIF007

Course : M.Sc. Bioinformatics

Exam : Practical Exam 2021-22

Paper code : BIM108

Date : 07.05.2022

Q.2 Using an example of your own demonstrate the utility of the following tools:

A) Blast tool (Blastp only)

B) PSI-blast (3-5 iterations)

C) Multiple sequence Alignment tool (using 50 -100 sequences)

D) phylogenetic tree

E) Gene prediction tool (using the prokaryotic system)

F) UCSF Chimera tool

A. Blast tool (Blastp only).

Utility:

 Measure the quality of an alignment with an alignment score

 Determine the significance of an alignment with a statistical model
 Return alignments that pass user-defined score and significance thresholds
 A BLAST search enables a researcher to compare a query sequence with a database of
sequences, and identify library sequences that resemble the query sequence above a certain
threshold.
 Provides a statistical model to help evaluate the significance of a given alignment
 BLAST is fast, reliable and widely used in the biomedical research community

Method:

1. Retrieve protein sequence from NCBI.

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2. Set max target sequence 100 and run BLASTP with default parameters.

3. Observe the results.

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B. PSI-blast (3-5 iterations):

PSI-BLAST (Position-Specific Iterative Basic Local Alignment Search Tool) derives a position-
specific scoring matrix (PSSM) or profile from the multiple sequence alignment of sequences
detected above a given score threshold using protein–protein BLAST.
Background. PSI-BLAST, an extremely popular tool for sequence similarity search, features the
utilization of Position-Specific Scoring Matrix (PSSM) constructed from a multiple sequence
alignment (MSA). PSSM allows the detection of more distant homologs than a general amino
acid substitution matrix does.

Methods:
1. enter your query in psi-blast and change thesold from 0.005 to 0.0001.
2. then check the result and run 2 nd iteration.

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3. then run 3rd iteration.

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C) Multiple sequence Alignment tool (using 50 -100 sequences):

ClustalX features a graphical user interface and some powerful graphical utilities for aiding the
interpretation of alignments and is the preferred version for interactive usage.

The Clustal programs are widely used for carrying out automatic multiple alignment of nucleotide or
amino acid sequences. The most familiar version is ClustalW, which uses a simple text menu system
that is portable to more or less all computer systems. ClustalX features a graphical user interface and
some powerful graphical utilities for aiding the interpretation of alignments and is the preferred
version for interactive usage. Users may run Clustal remotely from several sites using the Web or the
programs may be downloaded and run locally on PCs, Macintosh, or Unix computers.

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Method:

1. Download all the fasta format in asingle text file.

2. Align that file in cliustalx.
3. Observe the conserved regions and gaps.

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D) phylogenetic tree

Clustal Omega is a multiple sequence alignment program for aligning three or more sequences
together in a computationally efficient and accurate manner. It produces biologically meaningful
multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via
viewing Cladograms or Phylograms.

Method:

1. Go to Clustal omega site and enter all the fasta formts and observe the phylogenetic tree.

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E) Gene prediction tool (using the prokaryotic system):

In bioinformatics, GENSCAN is a program to identify complete gene structures in genomic DNA. It is a

GHMM-based program that can be used to predict the location of genes and their exon-intron
boundaries in genomic sequences from a variety of organisms. The GENSCAN Web server can be
found at MIT.

Method:

1. go to ncbi and download gene sequence in fasta format.

2. go to genscan online tool and upload ayour fasta format.

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 3. it will show the following output.

F) UCSF Chimera tool:

UCSF Chimera is a program for the interactive visualization and analysis of molecular structures and
related data, including density maps, trajectories, and sequence alignments. It is available free of
charge for noncommercial use.

Method:

1. open pdb and copy pdb id

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2. enter pdb id in chimera and visualize the molecule.

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