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Bioinformatics pp 225–269Cite as

Genomic Database Searching

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

Abstract

The availability of reference genome sequences for virtually all species under active research has revolutionized biology. Analyses of genomic variations in many organisms have provided insights into phenotypic traits, evolution and disease, and are transforming medicine. All genomic data from publicly funded projects are freely available in Internet-based databases, for download or searching via genome browsers such as Ensembl, Vega, NCBI’s Map Viewer, and the UCSC Genome Browser. These online tools generate interactive graphical outputs of relevant chromosomal regions, showing genes, transcripts, and other genomic landmarks, and epigenetic features mapped by projects such as ENCODE.

This chapter provides a broad overview of the major genomic databases and browsers, and describes various approaches and the latest resources for searching them. Methods are provided for identifying genomic locus and sequence information using gene names or codes, identifiers for DNA and RNA molecules and proteins; also from karyotype bands, chromosomal coordinates, sequences, motifs, and matrix-based patterns. Approaches are also described for batch retrieval of genomic information, performing more complex queries, and analyzing larger sets of experimental data, for example from next-generation sequencing projects.

Key words

  • Bioinformatics
  • Epigenetics
  • Genome browsers
  • Identifiers
  • Internet-based software
  • Next-generation sequencing
  • Motifs
  • Matrices
  • Sequences

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Abbreviations

API:

Application Programming Interface

BED:

Browser Extensible Data

BLAST:

Basic Local Alignment Search Tool

BLAT:

BLAST-Like Alignment Tool

DDBJ:

DNA Databank of Japan

EBI:

European Bioinformatics Institute

EMBOSS:

European Molecular Biology Open Software Suite

ENA:

European Nucleotide Archive

ENCODE:

Encyclopedia Of DNA Elements

FTP:

File Transfer Protocol

GI:

GenInfo Identifier

GOLD:

Genomes Online Database

GRC:

Genome Reference Consortium

GUI:

Graphical User Interface

HAVANA:

Human and Vertebrate Analysis and Annotation

ID:

Identifier Code

INSDC:

International Nucleotide Sequence Database Collaboration

NCBI:

National Center for Biotechnology Information

NGS:

Next-Generation Sequencing

PWM:

Position Weight Matrix

RegEx:

Regular Expression

REST:

Representational State Transfer

ROI:

Region of Interest

RSAT:

Regulatory Sequence Analysis Tools

UCSC:

University of California Santa Cruz

URL:

Uniform Resource Locator

Vega:

Vertebrate Genome Annotation

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Acknowledgements

I would like to thank the numerous developers and support staff of genomic databases who provided valuable information during the researching and writing of this chapter. Grateful thanks also go to colleagues past and present who provided helpful information and advice. During the preparation of this chapter I worked in the laboratory of Dr. M. Méchali, whom I gratefully acknowledge for his guidance and support. I was supported financially by La Fondation pour la Recherche Médicale (FRM), and by the Centre National de la Recherche Scientifique (CNRS).

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  1. Institute of Human Genetics (IGH), CNRS, 141 rue de la Cardonille, 34396, Montpellier, France

    James R. A. Hutchins

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  1. James R. A. Hutchins
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Correspondence to James R. A. Hutchins .

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  1. Monash University, Melbourne, Victoria, Australia

    Jonathan M. Keith

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Hutchins, J.R.A. (2017). Genomic Database Searching. 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_10

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  • DOI: https://doi.org/10.1007/978-1-4939-6622-6_10

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