Advertisement

Computer Assisted Analysis of Genes

  • M. Victoria Fachal
  • Michael Furlan
Chapter

The overwhelming volume of molecular data generated over the last 30 years and the need to understand the messages coded by DNA has lead to the development of global bioinformatics resources. The scientific community has collaborated worldwide toward developing and linking computer database DNA and protein repositories and providing computer-based analysis tools that are publicly available on the Internet. Central to these collaborations are institutions such as the National Institutes of Health (NIH) in the United States, which created the National Center for Biotechnology Information (NCBI) and the European Molecular Biology Laboratory (EMBL) located in England that created the European Bioinformatics Institute (EBI). This chapter is a general introduction to using Internet based computing resources to support research in molecular biology. An overview of four popular biological data retrieval systems and five commonly used computer-based molecular analysis tools are discussed.

Keywords

European Bioinformatics Institute European Molecular Biology Laboratory Global Ocean Sampling Reverse Translate Universal Protein Resource 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Glossary of Terms and Acronyms

%GC:

percentage of guanine and cytosine

BLAST:

basic local alignment search tools

CDD:

conserved domain database

cDNA:

complementary DNA

DDBJ:

DNA database of Japan

EBI:

European Bioinformatics Institute

EMBL:

European Molecular Biology Laboratory

EMBOSS:

The European Molecular Biology Open Software Suite

ESTs:

expressed sequence tag

ExPASy:

expert protein analysis system

GOS:

global ocean sampling expedition

NCBI:

National Center for Biotechnology Information

NIH:

National Institutes of Health

OKdb:

Ovarian Kaleidoscope database

PCR:

polymerase chain reaction

PIR:

protein information resources

SIB:

Swiss Institute of Bioinformatics

SNP:

single nucleotide polymorphism

Tm:

melting temperature

UniMES:

UniProt metagenomic and environmental sequence database

UniParc:

UniProt archive

UniProt:

universal protein resource

UniProtKB:

UniProt knowledgebase

UniRef:

UniProt reference clusters

Bibliography

  1. 1.
    Geer RC, Sayers EW. Entrez making use of its power. Brief Bioinform 2003; 4:179–84.PubMedCrossRefGoogle Scholar
  2. 2.
    Ostell J. ‘The Entrez search retrieval system’ in ‘The NCBI Handbook’ [Internet], National Library of Medicine US 2002, chapter 14.Google Scholar
  3. 3.
    Benson DA, Karsch-Mizrachi I, Lipman DJ, et al. GenBank. ucleic Acids Res 2008; 36:25–30.CrossRefGoogle Scholar
  4. 4.
    Bairoch A, Apweiler R, Wu CH, et al. The Universal Protein Resource (UniProt) Nucleic Acids Res 2005; 33:154–9.CrossRefGoogle Scholar
  5. 5.
    Ben-Shlomo I, Vitt UA, Hsueh AJW. Perspective: The ovarian kaleidoscope database-II. Functional genomic analysis of an organ-specific database. Endocrinology 2002; 143:2041–4.PubMedCrossRefGoogle Scholar
  6. 6.
    Leo CP, Vitt UA, Hsueh AJW. The ovarian kaleidoscope database: An online resource for the ovarian research community. Endocrinology 2000; 141:3052–4.PubMedCrossRefGoogle Scholar
  7. 7.
    Altschul, SF, Madden TL, Schaeffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389–402.PubMedCrossRefGoogle Scholar
  8. 8.
    Korf I, Yandell M, Bedell J. BLAST, first edition. Sebastopol: O’Reilsly & Associates Inc, 2003.Google Scholar
  9. 9.
    Chenna R, Sugawara H, Koike T, et al. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 2003; 31:3497–500.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  1. 1.Department of BiologyUniversity of Saskatchewan College of Art and SciencesSaskatoonCanada
  2. 2.Novozymes BiologicalsSaskatoonCanada

Personalised recommendations