Computational biology - Revision history

Masini at 00:39, 14 March 2010

2010-03-14T00:39:14Z

Mfursov: adding reference to UGENE project to the software project list

2009-02-13T11:54:15Z

adding reference to UGENE project to the software project list

WikiSysop at 07:26, 23 December 2007

2007-12-23T07:26:22Z

WikiSysop at 07:24, 23 December 2007

2007-12-23T07:24:38Z

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Thkim at 01:58, 22 September 2007

2007-09-22T01:58:46Z

J at 16:28, 7 September 2007

2007-09-07T16:28:58Z

WikiSysop: Protected "Computational biology" [edit=autoconfirmed:move=autoconfirmed]

2007-06-10T07:42:26Z

Protected "Computational biology" [edit=autoconfirmed:move=autoconfirmed]

WikiSysop at 07:42, 10 June 2007

2007-06-10T07:42:20Z

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58.147.0.227 at 16:21, 8 June 2007

2007-06-08T16:21:30Z

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J at 04:26, 15 May 2007

2007-05-15T04:26:32Z

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@@ Line 9: / Line 9: @@
 <p><strong>Major research areas</strong></p>
 <p><strong>Sequence analysis</strong><br />
-Since the [[Phi-X174 phage|Phage &amp;Phi;-X174]] was [[sequencing|sequenced]] in 1977, the [[DNA sequence]]s of more and more organisms have been decoded and stored in electronic databases. This data is analyzed to determine genes that code for [[protein]]s, as well as regulatory sequences. A comparison of genes within a [[species]] or between different species can show similarities between protein functions, or relations between species (the use of [[molecular systematics]] to construct [[phylogenetic tree]]s). With the growing amount of data, it long ago became impractical to analyze DNA sequences manually. Today, [[computer program]]s are used to search the [[genome]] of thousands of organisms, containing billions of [[nucleotide]]s.&nbsp; These programs can compensate for mutations (exchanged, deleted or inserted bases) in the DNA sequence, in order to identify sequences that are related, but not identical. A variant of this [[sequence alignment]] is used in the sequencing process itself. The so-called [[shotgun sequencing]] technique (which was used, for example, by [[The Institute for Genomic Research]] to sequence the first bacterial genome, ''Haemophilus influenza'') does not give a sequential list of nucleotides, but instead the sequences of thousands of small DNA fragments (each about 600-800 nucleotides long). The ends of these fragments overlap and, when aligned in the right way, make up the complete genome. Shotgun sequencing yields sequence data quickly, but the task of assembling the fragments can be quite complicated for larger genomes. In the case of the [[Human Genome Project]], it took several months of CPU time (on a circa-2000 vintage DEC Alpha computer) to assemble the fragments.&nbsp; Shotgun sequencing is the method of choice for virtually all genomes sequenced today, and [[genome assembly]] algorithms are a critical area of bioinformatics research.</p>
+Since the [[Phi-X174 phage|Phage &amp;Phi;-X174]] was [[sequencing|sequenced]] in 1977, the [[DNA sequence]]s of more and more organisms have been decoded and stored in electronic databases. This data is analyzed to determine genes that code for [[protein]]s, as well as regulatory sequences. A comparison of genes within a [[species]] or between different species can show similarities between protein functions, or relations between species (the use of [[molecular systematics]] to construct [[phylogenetic tree]]s).<a rel="dofollow" href="http://www.all-auto.ro/dezmembrari-auto" title="dezmembrari masini"><img src="http://www.all-auto.ro/images/dezmembrari auto" alt="dezmembrari masini" hspace="2" vspace="2" border="0" /></a> With the growing amount of data, it long ago became impractical to analyze DNA sequences manually. Today, [[computer program]]s are used to search the [[genome]] of thousands of organisms, containing billions of [[nucleotide]]s.&nbsp; These programs can compensate for mutations (exchanged, deleted or inserted bases) in the DNA sequence, in order to identify sequences that are related, but not identical. A variant of this [[sequence alignment]] is used in the sequencing process itself. The so-called [[shotgun sequencing]] technique (which was used, for example, by [[The Institute for Genomic Research]] to sequence the first bacterial genome, ''Haemophilus influenza'') does not give a sequential list of nucleotides, but instead the sequences of thousands of small DNA fragments (each about 600-800 nucleotides long). The ends of these fragments overlap and, when aligned in the right way, make up the complete genome. Shotgun sequencing yields sequence data quickly, but the task of assembling the fragments can be quite complicated for larger genomes. In the case of the [[Human Genome Project]], it took several months of CPU time (on a circa-2000 vintage DEC Alpha computer) to assemble the fragments.&nbsp; Shotgun sequencing is the method of choice for virtually all genomes sequenced today, and [[genome assembly]] algorithms are a critical area of bioinformatics research.</p>
 <p>Another aspect of bioinformatics in sequence analysis is the automatic [[gene finding|search for genes]] and regulatory sequences within a genome.&nbsp; Not all of the nucleotides within a genome are genes. Within the genome of higher organisms, large parts of the DNA do not serve any obvious purpose.&nbsp; This so-called [[junk DNA]] may, however, contain unrecognized functional elements. Bioinformatics helps to bridge the gap between genome and [[proteome]] projects, for example in the use of DNA sequence for protein identification.</p>
 <p><strong>See also</strong>:' [[sequence analysis]], [[sequence profiling tool]], [[sequence motif]].</p>
@@ Line 91: / Line 91: @@
 [http://www.open-bio.org/ Open Bioinformatics Foundation: umbrella non-profit organization supporting certain open-source projects in bioinformatics]<br />
 [http://ncbo.us National Center for Biomedical Ontology]<br />
 [http://www.jgi.doe.gov/ US Department of Energy Joint Genome Institute]</p>
 <p><strong>Software projects<br />

@@ Line 119: / Line 119: @@
 [http://bio.macfast.org/bide/ BiDE - The Bioinformatics Desktop Environment - An Open Source project to develop a&nbsp; compact Red Hat Linux-based single CD installation, which provides all the flavours of bioinformatics to your desktop]<br />
 [http://www.biocircle.org/bide BioCircle BiDE Page]<br />
-[http://www.ebioinformatics.org/ eBiotools: A software package that brings most of the Bioinformatics programs to the MacOSX]</p>
+[http://www.ebioinformatics.org/ eBiotools: A software package that brings most of the Bioinformatics programs to the MacOSX]<br />
 <p><strong>Comprehensive, Reviewed, Third-Party Course Lists</strong><br />
 [http://wbiomed.curtin.edu.au/teach/biochem/resources/Bioinformatics.html A long list of courses world wide].<br />

@@ Line 132: / Line 132: @@
 [http://www.comcen.com.au/~journals/bioinfo.htm Online Journal of Bioinformatics ]<br />
 [http://www.embnet.org/download/embnetnews/index.html EMBnet.News Online&nbsp; Journal]</p>
-<p><strong>Other Important Sites</strong></p>
+<p><strong>Other External Sites<br />
-<p>[http://www.biocircle.org/ OpenSource Bioinformatics / Computational Systems Biology portal]<br />
+</strong>[http://omics.org Omics.org]<br />
 [http://www.bionews.in/ Bioinformatics News]<br />
 [http://www.bioinfo-online.net/ Bioinfo-Online News]<br />
@@ Line 151: / Line 155: @@
 &nbsp;Mount, David W.&nbsp; ''Bioinformatics: Sequence and Genome Analysis'' Spring Harbor Press, May 2002. ISBN 0879696087<br />
 &nbsp;Pevzner, Pavel A. ''Computational Molecular Biology: An Algorithmic Approach'' The MIT Press, 2000. ISBN 0262161974</p>
-<p>{{genomics-footer}}<br />
+<p>&nbsp;</p>

← Older revision		Revision as of 01:58, 22 September 2007
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	[[Category:Bioinformatics\|*]]<br />		[[Category:Bioinformatics\|*]]<br />
	[[Category:Mathematical biology]]</p>		[[Category:Mathematical biology]]</p>
−	~~<p> </p>~~

@@ Line 1: / Line 1: @@
 <p><strong>Computational biology</strong> is biology that&nbsp;tries to solve biological problems using large amount of computational power and&nbsp;techniques from [[applied mathematics]], [[informatics]], [[statistics]], and [[computer science]].&nbsp;<br />
 <br />
-<strong>Bioinformatics and Compuational Biology</strong><br />
+<strong>[[Bioinformatics]] and Compuational Biology</strong><br />
 Bioinformatics is an independant dscipline that was&nbsp;formed around mid 1990s. While computational biology is a more generic field of biology where much computing resource is necessary. They are different from each other in many ways. Biological informatics is essentially the reverse of Computational Biology as it is an informatics field where the major application is biological problems.<br />
 <br />
@@ Line 79: / Line 79: @@
 <p>* [[applied mathematics]] &amp;mdash; [[biology]] &amp;mdash; [[computer science]] &amp;mdash; [[informatics]] &amp;mdash; [[mathematical biology]] &amp;mdash; [[theoretical biology]] &amp;mdash; [[Scientific computing]] &amp;mdash; [[cheminformatics]] &amp;mdash; [[computational science]]</p>
 <p><strong>External links</strong></p>
-<p>* [http://wikiomics.org Wikiomics.org: bioinformatics wiki] for users and developers of bioinformatics worldwide. Focused on practical questions and pointers towards both academic publications and software resources (opened November 2005). <!-- please use it instead of cluttering Wikipedia with links; that's the right place for most of the stuff below --></p>
+<p>[http://bioinformatics.ws Bioinformatics Wiki Site]<br />
 <p>* Major Societies<br />
 *[http://www.iscb.org/ The International Society for Computational Biology]</p>

← Older revision	Revision as of 07:42, 10 June 2007
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