BIF101 ASSIGNMENT NO. 2 SPRING 2023 || 100% RIGHT SOLUTION || CELL BIOLOGY || BY VuTech

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QUESTION-1

If you have a DNA sequence and you wish to search for other DNA sequences to find one that encodes the same or similar protein. Which of the five Basic Blast programs should you use?

SOLUTION:

If you have a DNA sequence and you want to search for other DNA sequences that encode the same or similar protein, you should use the Basic Local Alignment Search Tool (BLAST) program called "tblastn."

The tblastn program is specifically designed to search for protein-coding DNA sequences (nucleotide sequences) that align well with a protein query sequence. It translates the DNA sequence in all six reading frames and compares it to a protein database, allowing you to identify DNA sequences that potentially encode the same or similar protein.

Using tblastn, you can detect DNA sequences with significant similarity to your protein of interest, even if the DNA sequence itself might not exhibit obvious similarity. This can be particularly useful when searching for homologous proteins in organisms with diverse genomes.

So, in summary, if you want to find DNA sequences that encode the same or similar protein as your query sequence, you should use the tblastn program.

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QUESTION-2:

Describe briefly the basic programs of blast?

SOLUTION:

Blast, short for Basic Local Alignment Search Tool, is a widely used program in bioinformatics for comparing biological sequences. It helps in identifying similarities between DNA or protein sequences and provides valuable insights into their functional and evolutionary relationships. Here are the basic programs of Blast:

BLASTN:

This program is used to compare nucleotide sequences (DNA or RNA) against a database of nucleotide sequences. BLASTN identifies regions of similarity by performing local alignment searches, allowing for mismatches and gaps.

BLASTP:

BLASTP is designed to compare a protein sequence against a database of protein sequences. It uses a scoring system to find similarities and alignments between amino acid sequences. BLASTP is particularly useful in studying protein structure and function.

BLASTX:

BLASTX is used to compare a nucleotide sequence against a protein sequence database. It translates the DNA sequence in six frames and performs a comparison to find similarities between the translated protein sequences and the database. BLASTX is beneficial for identifying open reading frames and potential protein coding regions.

TBLASTN:

TBLASTN is the reverse of BLASTX. It compares a protein sequence against a nucleotide sequence database. TBLASTN translates the nucleotide sequence in six frames and searches for similarities between the translated protein sequences and the database. This program is helpful when searching for potential coding regions in a genome.

TBLASTX:

TBLASTX combines the concepts of BLASTX and TBLASTN. It compares a nucleotide sequence against a nucleotide database using a translated nucleotide query. This program is useful when searching for similarities between nucleotide sequences that may not be apparent at the DNA level.

These are the basic programs of Blast, each tailored for specific types of sequence comparisons. They have revolutionized the field of genomics and proteomics, allowing researchers to analyze vast amounts of biological data and gain insights into the functions and relationships of genes and proteins.

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