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Bioinformatics

Overview of attention for book
Cover of 'Bioinformatics'

Table of Contents

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    Book Overview
  2. Altmetric Badge
    Chapter 1 Genome Sequencing.
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    Chapter 2 Sequence Assembly.
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    Chapter 3 A Practical Approach to Protein Crystallography.
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    Chapter 4 Managing Sequence Data.
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    Chapter 5 Genome Annotation.
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    Chapter 6 Working with Ontologies.
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    Chapter 7 The Classification of Protein Domains.
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    Chapter 8 Multiple Sequence Alignment.
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    Chapter 9 Large-Scale Sequence Comparison.
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    Chapter 10 Genomic Database Searching.
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    Chapter 11 Finding Genes in Genome Sequence.
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    Chapter 12 Sequence Segmentation with changeptGUI.
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    Chapter 13 Measuring Natural Selection.
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    Chapter 14 Inferring Trees.
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    Chapter 15 Identifying Optimal Models of Evolution.
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    Chapter 16 Scaling Up the Phylogenetic Detection of Lateral Gene Transfer Events.
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    Chapter 17 Detecting and Analyzing Genetic Recombination Using RDP4.
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    Chapter 18 Species Tree Estimation from Genome-Wide Data with guenomu.
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    Chapter 19 Erratum to: Sequence Segmentation with changeptGUI
Attention for Chapter 9: Large-Scale Sequence Comparison.
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Chapter title
Large-Scale Sequence Comparison.
Chapter number 9
Book title
Bioinformatics
Published in
Methods in molecular biology, January 2017
DOI 10.1007/978-1-4939-6622-6_9
Pubmed ID
27896723
Book ISBNs
978-1-4939-6620-2, 978-1-4939-6622-6
Authors

Devi Lal, Mansi Verma

Editors

Jonathan M. Keith

Abstract

There are millions of sequences deposited in genomic databases, and it is an important task to categorize them according to their structural and functional roles. Sequence comparison is a prerequisite for proper categorization of both DNA and protein sequences, and helps in assigning a putative or hypothetical structure and function to a given sequence. There are various methods available for comparing sequences, alignment being first and foremost for sequences with a small number of base pairs as well as for large-scale genome comparison. Various tools are available for performing pairwise large sequence comparison. The best known tools either perform global alignment or generate local alignments between the two sequences. In this chapter we first provide basic information regarding sequence comparison. This is followed by the description of the PAM and BLOSUM matrices that form the basis of sequence comparison. We also give a practical overview of currently available methods such as BLAST and FASTA, followed by a description and overview of tools available for genome comparison including LAGAN, MumMER, BLASTZ, and AVID.

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Mendeley readers

The data shown below were compiled from readership statistics for 18 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 18 100%

Demographic breakdown

Readers by professional status Count As %
Other 3 17%
Student > Ph. D. Student 3 17%
Researcher 3 17%
Student > Master 2 11%
Lecturer 1 6%
Other 0 0%
Unknown 6 33%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 5 28%
Computer Science 3 17%
Agricultural and Biological Sciences 2 11%
Unknown 8 44%

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