Introduction to Bioinformatics — NCERT Solutions

Answer:

The two major classes of biological macromolecules are:

1. Nucleic Acids – These include DNA (Deoxyribonucleic acid) and RNA (Ribonucleic acid). They store and transmit genetic information and play a central role in protein synthesis.

2. Proteins – These are polymers of amino acids and perform a vast array of functions in the cell, including catalysis (enzymes), structural support, transport, and signalling.

(Other acceptable answers: Carbohydrates and Lipids.)

Correct Option: (d) All of the above

Justification:

DNA sequences can be represented in all three formats:

• (a) FASTQ – A text-based format that stores both the nucleotide sequence and its corresponding quality scores. It is the standard output format from Next Generation Sequencing (NGS) platforms.

• (b) FASTA – A simple text-based format that represents nucleotide or protein sequences using single-letter codes. It begins with a '>' header line followed by the sequence.

• (c) AB1 – A binary file format produced by Sanger sequencing instruments (e.g., Applied Biosystems). It contains the raw chromatogram data along with the called DNA sequence.

Hence, all of the above formats can be used to represent DNA sequences.

Answer: No, a phylogeny cannot be produced directly from a multi-fasta file.

Justification:

A multi-FASTA file contains multiple sequences in FASTA format (each with a '>' header and its sequence), but these sequences are not aligned to each other.

To construct a phylogenetic tree (phylogeny), the following steps are required:

Step 1 – Multiple Sequence Alignment (MSA): The sequences in the multi-FASTA file must first be aligned using tools such as ClustalW, MUSCLE, or MAFFT. This alignment identifies homologous positions across all sequences.

Step 2 – Phylogenetic Analysis: Only after alignment can a phylogenetic tree be constructed using methods such as:

• Neighbour-Joining (NJ)
• Maximum Likelihood (ML)
• Bayesian Inference

Using tools like MEGA, PhyML, or RAxML.

Conclusion: A multi-FASTA file is a prerequisite (raw input), but it must undergo multiple sequence alignment first before a phylogeny can be generated. Therefore, a phylogeny cannot be produced directly from an unaligned multi-FASTA file.

Correct Option: (b) CIRCOS

Justification:

CIRCOS is a software tool specifically designed to visualise genomic data in a circular layout. It is widely used to display chromosomal relationships, structural variants, copy number variations, and other genomic features in a circular, visually informative manner.

• UCSC Genome Browser displays genomic data in a linear track-based format.
• IGV (Integrative Genomics Viewer) also displays genomic data in a linear format and is used to visualise read alignments and variants along a reference genome.

Hence, CIRCOS is the correct tool for circular visualisation of variants.

Answer:

Why do we need to sequence nucleic acids?

Nucleic acids (DNA and RNA) carry the fundamental genetic information of all living organisms. Sequencing nucleic acids allows us to read this information at the molecular level. The need to sequence nucleic acids arises because:

1. The sequence of DNA determines the sequence of proteins, which in turn determines the structure and function of cells and organisms.
2. Variations in nucleic acid sequences are responsible for genetic diseases, evolutionary differences, and individual traits.
3. Understanding gene expression (via RNA sequencing) helps us know which genes are active under specific conditions.

What can one gain by understanding the sequence of nucleic acids?

By understanding the sequence of nucleic acids, one can gain the following:

1. Gene identification: Locate and identify genes within a genome, including their regulatory regions.

2. Understanding genetic diseases: Identify mutations, SNPs, InDels, and other variants responsible for hereditary or acquired diseases (e.g., cancer, sickle cell anaemia).

3. Evolutionary studies: Compare sequences across species to understand evolutionary relationships and construct phylogenetic trees.

4. Drug and vaccine development: Identify target genes/proteins in pathogens for the development of new drugs, vaccines, and diagnostic tools.

5. Transcriptomics: RNA sequencing reveals gene expression patterns, helping understand how organisms respond to environmental changes, diseases, or developmental stages.

6. Personalised medicine: Understanding an individual's genomic sequence enables tailored medical treatments based on their genetic makeup.

7. Forensic science: DNA sequencing is used in forensic identification and paternity testing.

In summary, sequencing nucleic acids is fundamental to modern biology and medicine, providing insights into the blueprint of life, disease mechanisms, and evolutionary history.