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Large-Scale Sequence Comparison

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Bioinformatics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1525))

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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Author information

Authors and Affiliations

  1. Ramjas College, University of Delhi, New Delhi, 110 007, India

    Devi Lal

  2. Sri Venkateswara College, University of Delhi (South Campus), Benito Juarez Road, Dhaula Kuan, New Delhi, 110 021, India

    Mansi Verma

Authors
  1. Devi Lal
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  2. Mansi Verma
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Corresponding author

Correspondence to Mansi Verma .

Editor information

Editors and Affiliations

  1. Monash University, Melbourne, Victoria, Australia

    Jonathan M. Keith

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© 2017 Springer Science+Business Media New York

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Lal, D., Verma, M. (2017). Large-Scale Sequence Comparison. In: Keith, J. (eds) Bioinformatics. Methods in Molecular Biology, vol 1525. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6622-6_9

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  • DOI: https://doi.org/10.1007/978-1-4939-6622-6_9

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6620-2

  • Online ISBN: 978-1-4939-6622-6

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