Bioinformatics FAQ

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''We're in the process of moving the subsections to separate articles.  Please pardon the mess.''
 
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==Bioinformatics==
==Bioinformatics==
[[Bioinformatics|What is bioinformatics?]]
[[Bioinformatics|What is bioinformatics?]]
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[[Origins Of Bioinformatics|What are the origins of bioinformatics?]]
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[[Origins of bioinformatics|What are the origins of bioinformatics?]]
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[[Common Programs|What are the most common bioinformatics programs?]]
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[[Common programs|What are the most common bioinformatics programs?]]
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[[Common Technologies|What are the most common bioinformatics technologies?]]
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[[Common technologies|What are the most common bioinformatics technologies?]]
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[[Data Analysis|How are data analyzed in bioinformatics?]]
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[[Data analysis|How are data analyzed in bioinformatics?]]
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==Fields Related to Bioinformatics==
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==Fields related to bioinformatics==
[[Biophysics|What is biophysics?]]
[[Biophysics|What is biophysics?]]
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[[Computational Biology|What is computational biology?]]
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[[Computational biology|What is computational biology?]]
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[[Medical Informatics|What is medical informatics?]]
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[[Medical informatics|What is medical informatics?]]
[[Cheminformatics|What is cheminformatics?]]
[[Cheminformatics|What is cheminformatics?]]
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[[Genomics|What is genomics?]]
[[Genomics|What is genomics?]]
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[[Mathematical Biology|What is mathematical biology?]]
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[[Mathematical biology|What is mathematical biology?]]
[[Proteomics|What is proteomics?]]
[[Proteomics|What is proteomics?]]
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==Books: Can you recommend any bioinformatics books?==
==Books: Can you recommend any bioinformatics books?==
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It's notoriously difficult to find any books on bioinformatics itself that cater well for all of those coming from computing, from mathematics and from biology backgrounds. The few textbooks available in the field tend to be eyewateringly expensive as well. I've divided suggested reading into [#generalBooks books of general interest], [#computerScientistsBooks those] best suited to people coming from a computational/mathematical background and [#biologistsBooks books for biologists interested in bioinformatics]. After my suggestions are some links to other lists of bioinformatics books.
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See [[Recommended books|this article]].
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===General introductions===
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==Centers of bioinformatics activity: Where is bioinformatics done?==
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Many people are curious about the Human Genome (Project). The completion of the first draft probably represents bioinformatics' coming of age as a discipline. The first couple of books are aimed at the intelligent layperson.
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[http://www.rfcgr.mrc.ac.uk/GenomeWeb/ Genome Web] at the [http://www.rfcgr.mrc.ac.uk/ Rosalind Franklin Centre for Genomics Research] at the [http://www.hinxton.wellcome.ac.uk/ Genome Campus] near [http://www.cambridge.gov.uk/cambridge.htm Cambridge], UK, provides some of the links below.
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A gossipy and insightful account of the race to sequence the genome can be found in "<cite>The Sequence</cite>" by Kevin Davies [Weidenfeld; ISBN 0297646982]. Matt Ridley's "<cite>Genome</cite>" [Fourth Estate; ISBN 185702835X] is both an interesting layperson's introduction to the issues raised by the bioinformatic revolution and an overview of its biology and enormous scope. If I remember rightly, Ridley's book received a slightly snooty review from Walter Bodmer. This is understandable, since his and Robin McKie's excellent "pre-genomic" guide to the Human Genome Mapping Project, "The Book of Life" [Oxford Paperbacks; ISBN 0195114876] was undeservedly in a remainders bin when I bought my copy a couple of years ago.
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[[Research centers]]
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If you are a non-biological scientist (or a non-scientist) and are hooked by these, why not go back to the "real beginning" of the race and read James Watson's entertaining and indiscreet memoir of his and Francis Crick's determination of the structure of DNA, "<cite>The Double Helix</cite>" [Penguin; ISBN 0140268774]---now updated with an introduction by media don Steve Jones.
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[[Sequencing centers]]
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Nigel Barber at Peterborough Regional College in the UK recommends Gary Zweiger's "Transducing the Genome" [McGraw-Hill Professional Publishing: ISBN 0071369805]. The [http://www.amazon.com/exec/obidos/ASIN/0071369805/ summary] at Amazon makes it sound a tad pretentious, but all the reviews seem pretty positive so it might be worth a read.
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[[Standard centers]]
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If you are a quantitative scientist and would like a deeper knowledge of contemporary (molecular) biology, but you want to acquire it as painlessly as possible you could try the following:
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[[Virtual centers for bioinformatics activity]]
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* Donna Rae Siegfried's <cite>Biology for Dummies</cite> [Wiley; ISBN 0-7645-5326-7] is fun, well thought out and a lot more informative than the title might suggest. If only all biology textbooks were this entertaining and unpretentious.
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==Online resources: What bioinformatics websites are there?==
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* If you already have some biological knowledge and would like to get a grip on modern biomolecular science then Richard J. Epstein's <cite>Human Molecular Biology</cite> is an elegant, colourful and detailed guide.
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===Computational/Mathematical aspects===
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If you are a hardcore maths/computing person Michael Waterman's <cite>"Introduction to Computational Biology"</cite> [Chapman & Hall/CRC Statistics and Mathematics; ISBN 0412993910] and Pavel Pevzner's <cite>"Computational Molecular Biology - An Algorithmic Approach"</cite> [The MIT Press (A Bradford Book); ISBN 0262161974] will give you all the discrete maths you can shake a stick at, but perfunctory introductions to the biology.
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Bioinformatics.Org's very own Jeff Bizzaro recommends Dan Gusfield's <cite>"Algorithms on Strings, Trees and Sequences"</cite> [Cambridge, 1997 ISBN 0-52158-519-8], Richard Durbin, S. Eddy, A. Krogh, G. Mitchison <cite>"Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids"</cite> [Cambridge, 1997 ISBN 0-52162-971-3] (which I think is one of the clearest and most comprehensive guides to alignment algorithms) and---for that full "computers-to-biology conversion"--- Geoffrey M. Cooper <cite>"The Cell: A Molecular Approach"</cite> [ASM Press, 1996 ISBN 0-87893-119-8]. Jeff Ames writes that a second edition of this book is now available [Sinauer Associates, Incorporated, 2000 ISBN 0-87893-106-6] and that this version---if you can find it in the shops---comes with a CD.
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===Applying bioinformatics to biological research===
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One outstanding general text for the biologist is David W. Mount's "<cite>Bioinformatics</cite>" [Cold Spring Harbor Press; ISBN 0879696087]. It's not cheap, but it's the best I've seen if you are studying bioinformatics ''itself''.
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Bioinformatics has been dismissed by some as "the science of BLAST searches". The best collection of advice so far on doing BLAST searches is [http://www.oreilly.com/ O'Reilly's] [http://www.oreilly.com/catalog/blast/ <cite>BLAST</cite>] book by Ian Korf, Mark Yandell and Joseph Bedell [O'Reilly ISBN 0-596-00299-8]. I reviewed it enthusiastically, but not uncritically, for the [http://www.ukuug.org/ UK UNIX Users' Group] magazine. I'd go as far as to say that all biologists thinking of using BLAST in their research should read the relevant sections before they even go near a computer.
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If you wish to use general bioinformatics ''tools'', especially if you are a little wary of computers, my new "best" book is "<cite>Bioinformatics for Dummies</cite>" [John Wiley and Sons ISBN 0764516965]. It is (obviously) aimed at people who are beginners, who are happier using the Web rather than typing commands, and who are more interested in learning than in impressing people---the writing is friendly clear and unpretentious. However, like several of my other tips (below) it concentrates on Web-based resources so it will, inevitably, date. (This is partially compensated for by there being [http://www.dummies.com/extras/bioinformatics_fd/ a companion Website].)
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Also, if you're coming to the subject as a computer user with a biological background, looking to exploit the many tools available, you might want to try Terry Attwood and David Parry-Smith's <cite>"Introduction to Bioinformatics"</cite> [Longman Higher Education; ISBN 0582327881], or Des Higgins and Willie Taylor's <cite>"Bioinformatics: Sequence Structure and Databanks"</cite> [Oxford University Press; ISBN 0199637903]. Another excellent practical introduction is Andreas Baxevanis and Francis Oulette's "<cite>Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins</cite>" [Wiley-Interscience; ISBN 0471383910], now in its new and improved second edition. Bax teaches bioinformatics all over Canada and the experience shows.
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Bioinformatics.Org also recommends Cynthia Gibas and Per Jambeck's <cite>"Developing Bioinformatics Skills"</cite> [O'Reilly, 2001 ISBN 1-56592-664-1].
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Stuart Brown recommends his own book <cite>"Bioinformatics: A Biologist's Guide to Biocomputing and the Internet"</cite> [Eaton Pub Co; ISBN: 188129918X]. If he sends me a review copy I might recommend it too ;-) .
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===Fiction books===
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<cite>"Darwin's Radio"</cite> by Greg Bear [Ballantine Books, ISBN: 0345435249] is a wonderful hard SF thriller which stretches ideas derived from genome discoveries to their breaking point. It's gripping and humane.
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Leonard Crane, the author of <cite>[http://www.ninthday.com/ Ninth Day of Creation]</cite> kindly sent me a copy for review. So far it's an excellent read. I haven't finished it yet, not because it isn't a rattling good story, but because, like <cite>"Darwin's Radio"</cite>, it is very long and because I am very busy. If you'd like to read a well-researched, but speculative, novel containing actual scenes of practising bioinformatics then try it.
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Ken Allen contributed the following reviews:
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<blockquote>
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"<cite>Frameshift</cite> [Tor Books, ISBN: 0812571088] by Robert J. Sawyer---based around the HGP---reasonable read, but poor / confused ending."
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</blockquote><blockquote>
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<cite>Calculating God</cite> [Tor Books, ISBN: 0812580354]by the same author---has a subtler bio connection and is a much better read. Near the start an alien spacecraft lands, the alien emerges and says 'take me to your paleontologist'
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</blockquote>
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===Other lists of bioinformatics books===
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See also [http://compbiology.org compbiology.org]'s [http://compbiology.org/?section=books list], Steve Brenner's [http://compbio.berkeley.edu/people/brenner/misc/books-compbio.html  list], and [http://www.brc.dcs.gla.ac.uk/%7Eactan/bioinformatics/BioinformaticsBooks.html Aik Choon Tan's collection of books].
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==Centres of Bioinformatics Activity: Where is bioinformatics done?==
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The biggest and best source of bioinformatics links I have encountered is the [http://www.rfcgr.mrc.ac.uk/GenomeWeb/ Genome Web] at the [http://www.rfcgr.mrc.ac.uk/ Rosalind Franklin Centre for Genomics Research] at the [http://www.hinxton.wellcome.ac.uk/ Genome Campus] near [http://www.cambridge.gov.uk/cambridge.htm Cambridge], UK. Most of the links below come from that resource. My list is necessarily limited by comparison.
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[[Research Centers]]
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[[Sequencing Centers]]
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[[Standard Centers]]
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[[Virtual Centers for Bioinformatics Activity]]
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==Online Resources: What bioinformatics Websites are there?==
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[[Blogs]]
[[Blogs]]
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[[Information]]
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[[General information websites]]
[[Directories]]
[[Directories]]
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[[Societies]]
[[Societies]]
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[[Collections of Tools]]
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[[Collections of tools]]
[[Portals]]
[[Portals]]
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[[Tutorials]]
[[Tutorials]]
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==Education: Where can I study Bioinformatics...==
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==Education: Where can I study bioinformatics?==
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This section is ''not'' complete, but contributions to broaden its coverage are welcome. '''Please do not direct questions about eligibility, course quality or admissions policy to me, but to ask the individual institutions directly.''' Use the links to obtain contact details. If an institution doesn't provide telephone numbers/email addresses or snailmail details on its Web site it doesn't deserve your patronage.
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This resource focuses on complete, full-time degree programmes rather than on individual study modules. Curating a list of the latter would be a full-time job. You can go to other places, however, if you are looking for short courses. Thanks to various [#acknowledgementsLinks contributors], including Wentian Li who pointed me to this [http://linkage.rockefeller.edu/wli/bioinfocourse/ list] at Rockefeller which is mirrored at various other sites. And to Humberto Ortiz Zuazaga for mailing me a link to the ICSB, where you can find [http://www.iscb.org/univ.shtml this list].
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If you are interested in U.S. programmes, here's [http://wbiomed.curtin.edu.au/teach/biochem/resources/Bioinformatics.html a list from Curtin] and here's [http://www.smi.stanford.edu/academics/pdfs/degree_table.pdf a list from Stanford]. Thanks to Amelie Stein who also supplied some of the individual entries in this section.
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Those wanting to find programmes in the Asia Pacific region could have a look at [http://www.apbionet.org/project/edu/index.shtml this resource] maintained by the Asia Pacific Bioinformatics Network APBioNet. Thanks to Sentausa.
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In the UK [http://www.rfcgr.mrc.ac.uk/CCP11/index.jsp The Bioinformatics Resource] (part of the [http://www.bbsrc.ac.uk/ BBSRC]'s [http://www.rfcgr.mrc.ac.uk/CCP11/index.jsp  CCP11] project) project maintains (among many other resources) lists of (mainly) British [http://www.rfcgr.mrc.ac.uk/CCP11/directory/directory_mastersdegrees.jsp?Rp=20  Masters] and [http://www.rfcgr.mrc.ac.uk/CCP11/directory/directory_phds.jsp?Rp=20  PhDs] in bioinformatics. If you have any suggestions or updates please [/sendmessage.php?toaddress=counsell_maillink_bioinformatics.org  contact] me with them. You can publicize your course and offer a public service at the same time.
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Below are complete, full-time degree programmes rather than on individual study modules. You can go to other places, however, if you are looking for short courses. Rockefeller has a [http://linkage.rockefeller.edu/wli/bioinfocourse/ list] that is mirrored at various other sites. ICSB also maintains a [http://www.iscb.org/univ.shtml list].
[[Africa]]
[[Africa]]
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[[Europe]]
[[Europe]]
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[[Distance or Correspondence Courses]]
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[[Distance or correspondence courses]]
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==Careers: How can I become a bioinformatician?==
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==Careers: How can I become a bioinformatics practitioner?==
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[[Getting Involved]]
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[[Getting involved]]
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[[Bioinformatics Jobs]]
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[[Careers]]
==Practical tips==
==Practical tips==
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This section includes some simple rules-of-thumb to apply when performing common bioinformatics tasks.  
This section includes some simple rules-of-thumb to apply when performing common bioinformatics tasks.  
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[[Finding a Sequence|Finding a sequence]]
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[[Finding a sequence]]
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[[Aligning Two Sequences|Aligning two sequences]]
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[[Sequence alignment|Aligning two sequences]]
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[[Predicting the Functions of a Gene|Predicting the functions of a gene]]
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[[Gene function prediction|Predicting the functions of a gene]]
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[[Predicting the Structure of a Sequence|Predicting the structure of a sequence]]
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[[Sequence structure prediction|Predicting the structure of a sequence]]
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[[Simulating a Biomolecule|Simulating a biomolecule]]
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[[Simulating a biomolecule]]
[[Publishing]]
[[Publishing]]
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==Glossary of bioinformatics terms==
==Glossary of bioinformatics terms==
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Here I attempt to define some common terms in bioinformatics. I have tried to balance clarity, brevity and rigour. Let me know if I let one of these priorities over-ride the others.
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Here are some common terms in bioinformatics:
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[[Sequence Alignment]]
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[[Sequence alignment]]
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[[DNA Array]]
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[[DNA array]]
[[Homologue]]
[[Homologue]]
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[[Ontology]]
[[Ontology]]
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[[Scoring Matrix]]
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[[Scoring matrix]]

Latest revision as of 03:00, 24 November 2010

Contents

Bioinformatics

What is bioinformatics?

What are the origins of bioinformatics?

What are the most common bioinformatics programs?

What are the most common bioinformatics technologies?

How are data analyzed in bioinformatics?

Fields related to bioinformatics

What is biophysics?

What is computational biology?

What is medical informatics?

What is cheminformatics?

What is genomics?

What is mathematical biology?

What is proteomics?

What is pharmacogenomics?

What is pharmacogenetics?

Books: Can you recommend any bioinformatics books?

See this article.

Centers of bioinformatics activity: Where is bioinformatics done?

Genome Web at the Rosalind Franklin Centre for Genomics Research at the Genome Campus near Cambridge, UK, provides some of the links below.

Research centers

Sequencing centers

Standard centers

Virtual centers for bioinformatics activity

Online resources: What bioinformatics websites are there?

Blogs

General information websites

Directories

Societies

Collections of tools

Portals

Tutorials

Education: Where can I study bioinformatics?

Below are complete, full-time degree programmes rather than on individual study modules. You can go to other places, however, if you are looking for short courses. Rockefeller has a list that is mirrored at various other sites. ICSB also maintains a list.

Africa

The Americas

Asia

Australia

Europe

Distance or correspondence courses

Careers: How can I become a bioinformatics practitioner?

Getting involved

Careers

Practical tips

This section includes some simple rules-of-thumb to apply when performing common bioinformatics tasks.

Finding a sequence

Aligning two sequences

Predicting the functions of a gene

Predicting the structure of a sequence

Simulating a biomolecule

Publishing

Glossary of bioinformatics terms

Here are some common terms in bioinformatics:

Sequence alignment

DNA array

Homologue

Ontology

Scoring matrix

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