Lecture 7 - NCBI: Similarity searching tool-BLAST | Bioinformatics - Botany PDF Download

 Page 1


NCBI: Similarity searching tool-BLAST 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
 
 
 
 
Subject: Bioinformatics 
Lesson: NCBI: Similarity searching tool-BLAST 
Lesson Developer: Sandipa Das 
College/ Department: Department of Botany, University of 
Delhi 
Page 2


NCBI: Similarity searching tool-BLAST 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
 
 
 
 
Subject: Bioinformatics 
Lesson: NCBI: Similarity searching tool-BLAST 
Lesson Developer: Sandipa Das 
College/ Department: Department of Botany, University of 
Delhi 
; 
Institute of Lifelong Learning, University of Delhi 1 
 
 
Table of Contents       
 
Chapter: NCBI: Similarity searching tool-BLAST                                 
? Introduction to Sequence Analysis 
 
? Sequence analysis tools 
? Similarity searching with nucleotide queries 
(BLASTN) 
? Similarity searching with Protein queries 
(BLASTP) 
? Summary  
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
 
 
 
 
 
 
 
 
 
Page 3


NCBI: Similarity searching tool-BLAST 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
 
 
 
 
Subject: Bioinformatics 
Lesson: NCBI: Similarity searching tool-BLAST 
Lesson Developer: Sandipa Das 
College/ Department: Department of Botany, University of 
Delhi 
; 
Institute of Lifelong Learning, University of Delhi 1 
 
 
Table of Contents       
 
Chapter: NCBI: Similarity searching tool-BLAST                                 
? Introduction to Sequence Analysis 
 
? Sequence analysis tools 
? Similarity searching with nucleotide queries 
(BLASTN) 
? Similarity searching with Protein queries 
(BLASTP) 
? Summary  
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
 
 
 
 
 
 
 
 
 
; 
Institute of Lifelong Learning, University of Delhi 2 
 
 
Introduction to Sequence Analysis 
Analysis of the sequence data is one of the major challenges of computation biology and is 
the first step towards understanding molecular basis of development and adaptation. 
Several types of analysis can be performed that range from  
DNA Sequence analysis 
? sequence similarity searches  
? prediction of genes and other genetic elements 
? evolutionary tendencies and trends 
? Functional information 
RNA analysis 
? Expression analysis 
? Structure 
? Functional information 
Protein level 
? Domain finding 
? Structure prediction 
? Evolution 
? Function 
Genome level 
? Comparative genomics 
? Genome organization and re-organisation 
? Genome annotation 
 
Similarity search with Nucleotide queries 
DNA sequence analysis constitutes one of the major applications in bioinformatics. Some of 
the basic objectives of performing sequence analyses are 
? Sequence retrieval 
? Finding similar sequence through similarity searching 
? Phylogenetic or evolutionary analysis 
? Finding homology relationships (orthologus and paralogous nature) 
? Discovering new genes and genetic elements 
Page 4


NCBI: Similarity searching tool-BLAST 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
 
 
 
 
Subject: Bioinformatics 
Lesson: NCBI: Similarity searching tool-BLAST 
Lesson Developer: Sandipa Das 
College/ Department: Department of Botany, University of 
Delhi 
; 
Institute of Lifelong Learning, University of Delhi 1 
 
 
Table of Contents       
 
Chapter: NCBI: Similarity searching tool-BLAST                                 
? Introduction to Sequence Analysis 
 
? Sequence analysis tools 
? Similarity searching with nucleotide queries 
(BLASTN) 
? Similarity searching with Protein queries 
(BLASTP) 
? Summary  
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
 
 
 
 
 
 
 
 
 
; 
Institute of Lifelong Learning, University of Delhi 2 
 
 
Introduction to Sequence Analysis 
Analysis of the sequence data is one of the major challenges of computation biology and is 
the first step towards understanding molecular basis of development and adaptation. 
Several types of analysis can be performed that range from  
DNA Sequence analysis 
? sequence similarity searches  
? prediction of genes and other genetic elements 
? evolutionary tendencies and trends 
? Functional information 
RNA analysis 
? Expression analysis 
? Structure 
? Functional information 
Protein level 
? Domain finding 
? Structure prediction 
? Evolution 
? Function 
Genome level 
? Comparative genomics 
? Genome organization and re-organisation 
? Genome annotation 
 
Similarity search with Nucleotide queries 
DNA sequence analysis constitutes one of the major applications in bioinformatics. Some of 
the basic objectives of performing sequence analyses are 
? Sequence retrieval 
? Finding similar sequence through similarity searching 
? Phylogenetic or evolutionary analysis 
? Finding homology relationships (orthologus and paralogous nature) 
? Discovering new genes and genetic elements 
; 
Institute of Lifelong Learning, University of Delhi 3 
? Exploring importance of residues (nucleotides and amino acids) that are 
important for structure and function 
Central to the process of searching for similar sequences from database and retrieval are 
concepts of homology that are derived from evolutionary relationships. DNA data can be 
used to retrieve similar sequences that have diverged upto 600 million years ago!  
Sequences can be retrieved from NCBI database by using the identity of the sequence in the 
form of accession number and/or using the “Identity” of the sequence as “query” to 
search against the entire database or by selecting a specific database. 
 
 
Figure NCBI homepage showing the location of the pull-down menu for accessing 
databases and search engine 
Page 5


NCBI: Similarity searching tool-BLAST 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
 
 
 
 
Subject: Bioinformatics 
Lesson: NCBI: Similarity searching tool-BLAST 
Lesson Developer: Sandipa Das 
College/ Department: Department of Botany, University of 
Delhi 
; 
Institute of Lifelong Learning, University of Delhi 1 
 
 
Table of Contents       
 
Chapter: NCBI: Similarity searching tool-BLAST                                 
? Introduction to Sequence Analysis 
 
? Sequence analysis tools 
? Similarity searching with nucleotide queries 
(BLASTN) 
? Similarity searching with Protein queries 
(BLASTP) 
? Summary  
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
 
 
 
 
 
 
 
 
 
; 
Institute of Lifelong Learning, University of Delhi 2 
 
 
Introduction to Sequence Analysis 
Analysis of the sequence data is one of the major challenges of computation biology and is 
the first step towards understanding molecular basis of development and adaptation. 
Several types of analysis can be performed that range from  
DNA Sequence analysis 
? sequence similarity searches  
? prediction of genes and other genetic elements 
? evolutionary tendencies and trends 
? Functional information 
RNA analysis 
? Expression analysis 
? Structure 
? Functional information 
Protein level 
? Domain finding 
? Structure prediction 
? Evolution 
? Function 
Genome level 
? Comparative genomics 
? Genome organization and re-organisation 
? Genome annotation 
 
Similarity search with Nucleotide queries 
DNA sequence analysis constitutes one of the major applications in bioinformatics. Some of 
the basic objectives of performing sequence analyses are 
? Sequence retrieval 
? Finding similar sequence through similarity searching 
? Phylogenetic or evolutionary analysis 
? Finding homology relationships (orthologus and paralogous nature) 
? Discovering new genes and genetic elements 
; 
Institute of Lifelong Learning, University of Delhi 3 
? Exploring importance of residues (nucleotides and amino acids) that are 
important for structure and function 
Central to the process of searching for similar sequences from database and retrieval are 
concepts of homology that are derived from evolutionary relationships. DNA data can be 
used to retrieve similar sequences that have diverged upto 600 million years ago!  
Sequences can be retrieved from NCBI database by using the identity of the sequence in the 
form of accession number and/or using the “Identity” of the sequence as “query” to 
search against the entire database or by selecting a specific database. 
 
 
Figure NCBI homepage showing the location of the pull-down menu for accessing 
databases and search engine 
; 
Institute of Lifelong Learning, University of Delhi 4 
 
 
Figure  An output window showing results obtained against all databases using “reverse 
transcriptase” as keyword using the Entrez system.