Bioinformatics pp 225-269 | Cite as

Genomic Database Searching

  • James R. A. HutchinsEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1525)


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 



Application Programming Interface


Browser Extensible Data


Basic Local Alignment Search Tool


BLAST-Like Alignment Tool


DNA Databank of Japan


European Bioinformatics Institute


European Molecular Biology Open Software Suite


European Nucleotide Archive


Encyclopedia Of DNA Elements


File Transfer Protocol


GenInfo Identifier


Genomes Online Database


Genome Reference Consortium


Graphical User Interface


Human and Vertebrate Analysis and Annotation


Identifier Code


International Nucleotide Sequence Database Collaboration


National Center for Biotechnology Information


Next-Generation Sequencing


Position Weight Matrix


Regular Expression


Representational State Transfer


Region of Interest


Regulatory Sequence Analysis Tools


University of California Santa Cruz


Uniform Resource Locator


Vertebrate Genome Annotation



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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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  1. 1.Institute of Human Genetics (IGH), CNRSMontpellierFrance

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