Sequence assembly - Revision history

http://pgi.re.kr/index.php?action=history&feed=atom&title=Sequence_assembly Sequence assembly - Revision history 2026-04-10T16:59:34Z Revision history for this page on the wiki MediaWiki 1.31.3 http://pgi.re.kr/index.php?title=Sequence_assembly&diff=3349&oldid=prev WikiSysop at 15:13, 18 December 2010 2010-12-18T15:13:53Z

<p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 15:13, 18 December 2010</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><p><span style="font-size: small"><span style="color: #000000">In bioinformatics, <b>sequence assembly</b> refers to aligning and merging fragments of a much longer DNA sequence in order to reconstruct the original sequence. This is needed as DNA sequencing technology cannot read whole genomes in one go, but rather small pieces between 20 and 1000 bases<del class="diffchange diffchange-inline">, depending on the technology used</del>. Typically the short fragments, called reads, result from shotgun sequencing genomic DNA, or gene transcript (<del class="diffchange diffchange-inline">ESTs</del>).</span></span></p></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><p><span style="font-size: small"><span style="color: #000000">In bioinformatics, <b>sequence assembly</b> refers to aligning and merging fragments of a much longer DNA sequence in order to reconstruct the original sequence. <ins class="diffchange diffchange-inline"></span></span></p></ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"><p><span style="font-size: small"><span style="color: #000000"></ins>This is needed as DNA sequencing technology cannot read whole genomes in one go, but rather small pieces between 20 and 1000 bases. <ins class="diffchange diffchange-inline"></span></span></p></ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"><p><span style="font-size: small"><span style="color: #000000"></ins>Typically the short fragments, called <ins class="diffchange diffchange-inline"><b></ins>reads<ins class="diffchange diffchange-inline"></b></ins>, result from shotgun sequencing genomic DNA, or gene transcript (<ins class="diffchange diffchange-inline">[[EST]]s</ins>).</span></span><ins class="diffchange diffchange-inline"></p></ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"><p><b><span style="font-size: small"><span style="color: #000000">Sequence assembly as reconstructing a book</span></span></b></p></ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"><p>&nbsp;</ins></p></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><p><span style="font-size: small"><span style="color: #000000">The problem of sequence assembly can be compared to taking many copies of a book, passing them all through a shredder, and piecing a copy of the book back together from only shredded pieces. The book may have many repeated paragraphs, and some shreds may be modified to have typos. Excerpts from another book may be added in, and some shreds may be completely unrecognizable.</span></span></p></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><p><span style="font-size: small"><span style="color: #000000">The problem of sequence assembly can be compared to taking many copies of a book, passing them all through a shredder, and piecing a copy of the book back together from only shredded pieces. The book may have many repeated paragraphs, and some shreds may be modified to have typos. Excerpts from another book may be added in, and some shreds may be completely unrecognizable.</span></span></p></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><p>&nbsp;</p></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><p>&nbsp;</p></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><h2><span style="color: #000000"><span id="Genome_assemblers" class="mw-headline">Genome assemblers</span></span></h2></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><h2><span style="color: #000000"><span id="Genome_assemblers" class="mw-headline">Genome assemblers</span></span></h2></div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><p><span style="font-size: small"><span style="color: #000000">The first sequence assemblers began to appear in the late 1980s and early 1990s as variants of simpler sequence alignment programs to piece together vast quantities of fragments generated by automated sequencing instruments called DNA sequencers. As the sequenced organisms grew in size and complexity <del class="diffchange diffchange-inline">(from small viruses over plasmids to bacteria and finally eukaryotes)</del>, the assembly programs needed to increasingly employ <del class="diffchange diffchange-inline">more and more </del>sophisticated strategies to handle:</span></span></p></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><p><span style="font-size: small"><span style="color: #000000">The first sequence assemblers began to appear in the late 1980s and early 1990s as variants of simpler sequence alignment programs to piece together vast quantities of fragments generated by automated sequencing instruments called DNA sequencers. <ins class="diffchange diffchange-inline"></span></span></p></ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"><p><span style="font-size: small"><span style="color: #000000"></ins>As the sequenced organisms grew in size and complexity, the assembly programs needed to increasingly employ sophisticated strategies to handle:</span></span></p></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><ul></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><ul></div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>     <li><span style="font-size: small"><span style="color: #000000">terabytes of <del class="diffchange diffchange-inline">sequencing </del>data which need processing on computing clusters;</span> </span></li></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>     <li><span style="font-size: small"><span style="color: #000000">terabytes of data which need processing on computing clusters;</span> </span></li></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     <li><span style="font-size: small"><span style="color: #000000">identical and nearly identical sequences (known as <i>repeats</i>) which can, in the worst case, increase the time and space complexity of algorithms exponentially;</span> </span></li></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     <li><span style="font-size: small"><span style="color: #000000">identical and nearly identical sequences (known as <i>repeats</i>) which can, in the worst case, increase the time and space complexity of algorithms exponentially;</span> </span></li></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     <li><span style="font-size: small"><span style="color: #000000">and errors in the fragments from the sequencing instruments, which can confound assembly.</span> </span></li></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     <li><span style="font-size: small"><span style="color: #000000">and errors in the fragments from the sequencing instruments, which can confound assembly.</span> </span></li></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></ul></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></ul></div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><p><span style="font-size: small"><span style="color: #000000">Faced with the challenge of assembling the first larger eukaryotic genomes, the fruit fly Drosophila melanogaster, in 2000 and the human genome <del class="diffchange diffchange-inline">just a year later</del>, scientists developed assemblers <del class="diffchange diffchange-inline">like </del>Celera Assembler<sup id="cite_ref-0" class="reference">[1]</sup> and Arachne<sup id="cite_ref-1" class="reference">[2]</sup> able to handle genomes of 100-300 <del class="diffchange diffchange-inline">million </del>base pairs. Subsequent to these efforts, several other groups, mostly at the major genome sequencing centers, built large-scale assemblers, and an open source effort known as AMOS<sup id="cite_ref-2" class="reference">[3]</sup> was launched to bring together all the innovations in genome assembly technology under the open source framework.</span></span></p></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><p><span style="font-size: small"><span style="color: #000000">Faced with the challenge of assembling the first larger eukaryotic genomes, the fruit fly <ins class="diffchange diffchange-inline">[[</ins>Drosophila melanogaster<ins class="diffchange diffchange-inline">]]</ins>, in <ins class="diffchange diffchange-inline"><b></ins>2000 <ins class="diffchange diffchange-inline"></b></ins>and the human genome <ins class="diffchange diffchange-inline">in <b>2001</b></ins>, scientists developed assemblers<ins class="diffchange diffchange-inline">&nbsp;such as&nbsp;</ins>Celera Assembler<sup id="cite_ref-0" class="reference">[1]</sup> and <ins class="diffchange diffchange-inline">[[</ins>Arachne<ins class="diffchange diffchange-inline">]]</ins><sup id="cite_ref-1" class="reference">[2]</sup> able to handle genomes of <ins class="diffchange diffchange-inline"><b></ins>100<ins class="diffchange diffchange-inline">,000,000 </ins>- 300<ins class="diffchange diffchange-inline">,000,000</b> </ins>base pairs. Subsequent to these efforts, several other groups, mostly at the major genome sequencing centers, built large-scale assemblers, and an open source effort known as <ins class="diffchange diffchange-inline">[[</ins>AMOS<ins class="diffchange diffchange-inline">]]</ins><sup id="cite_ref-2" class="reference">[3]</sup> was launched to bring together all the innovations in genome assembly technology under the open source framework.</span></span></p></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><h2><span style="font-size: medium"><span style="color: #000000"><span id="EST_assemblers" class="mw-headline">EST assemblers</span></span></span></h2></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><h2><span style="font-size: medium"><span style="color: #000000"><span id="EST_assemblers" class="mw-headline">EST assemblers</span></span></span></h2></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><p><span style="font-size: small"><span style="color: #000000">EST assembly differs from genome assembly in several ways. The sequences for EST assembly are the transcribed mRNA of a cell and represent only a subset of the whole genome. At a first glance, underlying algorithmical problems differ between genome and EST assembly. For instance, genomes often have large amounts of repetitive sequences, mainly in the inter-genic parts. Since ESTs represent gene transcripts, they will not contain these repeats. On the other hand, cells tend to have a certain number of genes that are constantly expressed in very high amounts (housekeeping genes), which again leads to the problem of similar sequences present in high amounts in the data set to be assembled.</span></span></p></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><p><span style="font-size: small"><span style="color: #000000">EST assembly differs from genome assembly in several ways. The sequences for EST assembly are the transcribed mRNA of a cell and represent only a subset of the whole genome. At a first glance, underlying algorithmical problems differ between genome and EST assembly. For instance, genomes often have large amounts of repetitive sequences, mainly in the inter-genic parts. Since ESTs represent gene transcripts, they will not contain these repeats. On the other hand, cells tend to have a certain number of genes that are constantly expressed in very high amounts (housekeeping genes), which again leads to the problem of similar sequences present in high amounts in the data set to be assembled.</span></span></p></div></td></tr>  </table>

WikiSysop http://pgi.re.kr/index.php?title=Sequence_assembly&diff=3348&oldid=prev WikiSysop at 15:10, 18 December 2010 2010-12-18T15:10:06Z

<p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 15:10, 18 December 2010</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l306" >Line 306:</td> <td colspan="2" class="diff-lineno">Line 306:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></table></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></table></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></p></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></p></div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><h2><span style="font-size: <del class="diffchange diffchange-inline">small</del>"><span style="color: #000000"><span id="See_also" class="mw-headline">See also</span></span></span></h2></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><h2><span style="font-size: <ins class="diffchange diffchange-inline">large</ins>"><span style="color: #000000"><span id="See_also" class="mw-headline">See also</span></span></span></h2></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><ul></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><ul></div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>     <li><span style="font-size: small"><span style="color: #000000">Sequence alignment</span> </span></li></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>     <li><span style="font-size: small"><span style="color: #000000"><ins class="diffchange diffchange-inline">[[</ins>Sequence alignment<ins class="diffchange diffchange-inline">]]</ins></span> </span></li></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     <li><span style="font-size: small"><span style="color: #000000">Genome assembly</span> </span></li></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     <li><span style="font-size: small"><span style="color: #000000">Genome assembly</span> </span></li></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></ul></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></ul></div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><h2><span style="font-size: <del class="diffchange diffchange-inline">small</del>"><span id="References" class="mw-headline">References</span></span></h2></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><h2><span style="font-size: <ins class="diffchange diffchange-inline">large</ins>"><span id="References" class="mw-headline">References</span></span></h2></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><ol class="references"></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><ol class="references"></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     <li id="cite_note-0"><span style="font-size: small"><b><a href="#cite_ref-0"><font color="#0645ad">^</font></a></b></span><span style="font-size: small"> <span class="citation Journal">Myers EW, Sutton GG, Delcher AL, <i>et al.</i> (March 2000). </span></span><span class="citation Journal"><span style="font-size: small"><a class="external text" rel="nofollow" href="http://www.sciencemag.org/cgi/pmidlookup?view=long&amp;pmid=10731133"><font color="#3366bb">&quot;A whole-genome assembly of Drosophila&quot;</font></a></span><span style="font-size: small">. <i>Science</i> <b>287</b> (5461): 2196&ndash;204. </span><span style="font-size: small"><a class="mw-redirect" title="PubMed Identifier" href="/wiki/PubMed_Identifier"><font color="#0645ad">PMID</font></a></span><span style="font-size: small">&nbsp;</span><span style="font-size: small"><a class="external text" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/pubmed/10731133"><font color="#3366bb">10731133</font></a></span><span style="font-size: small"><span class="printonly">. </span></span></span><span style="font-size: large"><span class="citation Journal"><span class="printonly"><a class="external free" rel="nofollow" href="http://www.sciencemag.org/cgi/pmidlookup?view=long&amp;pmid=10731133"><span style="font-size: small"><font color="#3366bb">http://www.sciencemag.org/cgi/pmidlookup?view=long&amp;pmid=10731133</font></span></a></span></span></span><span style="font-size: small"><span class="citation Journal">.</span><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=A+whole-genome+assembly+of+Drosophila&amp;rft.jtitle=Science&amp;rft.aulast=Myers+EW%2C+Sutton+GG%2C+Delcher+AL%2C+%27%27et+al.%27%27&amp;rft.au=Myers+EW%2C+Sutton+GG%2C+Delcher+AL%2C+%27%27et+al.%27%27&amp;rft.date=March+2000&amp;rft.volume=287&amp;rft.issue=5461&amp;rft.pages=2196%E2%80%93204&amp;rft_id=info:pmid/10731133&amp;rft_id=http%3A%2F%2Fwww.sciencemag.org%2Fcgi%2Fpmidlookup%3Fview%3Dlong%26pmid%3D10731133&amp;rfr_id=info:sid/en.wikipedia.org:Sequence_assembly"><span style="display: none">&nbsp;</span></span> </span></li></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     <li id="cite_note-0"><span style="font-size: small"><b><a href="#cite_ref-0"><font color="#0645ad">^</font></a></b></span><span style="font-size: small"> <span class="citation Journal">Myers EW, Sutton GG, Delcher AL, <i>et al.</i> (March 2000). </span></span><span class="citation Journal"><span style="font-size: small"><a class="external text" rel="nofollow" href="http://www.sciencemag.org/cgi/pmidlookup?view=long&amp;pmid=10731133"><font color="#3366bb">&quot;A whole-genome assembly of Drosophila&quot;</font></a></span><span style="font-size: small">. <i>Science</i> <b>287</b> (5461): 2196&ndash;204. </span><span style="font-size: small"><a class="mw-redirect" title="PubMed Identifier" href="/wiki/PubMed_Identifier"><font color="#0645ad">PMID</font></a></span><span style="font-size: small">&nbsp;</span><span style="font-size: small"><a class="external text" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/pubmed/10731133"><font color="#3366bb">10731133</font></a></span><span style="font-size: small"><span class="printonly">. </span></span></span><span style="font-size: large"><span class="citation Journal"><span class="printonly"><a class="external free" rel="nofollow" href="http://www.sciencemag.org/cgi/pmidlookup?view=long&amp;pmid=10731133"><span style="font-size: small"><font color="#3366bb">http://www.sciencemag.org/cgi/pmidlookup?view=long&amp;pmid=10731133</font></span></a></span></span></span><span style="font-size: small"><span class="citation Journal">.</span><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=A+whole-genome+assembly+of+Drosophila&amp;rft.jtitle=Science&amp;rft.aulast=Myers+EW%2C+Sutton+GG%2C+Delcher+AL%2C+%27%27et+al.%27%27&amp;rft.au=Myers+EW%2C+Sutton+GG%2C+Delcher+AL%2C+%27%27et+al.%27%27&amp;rft.date=March+2000&amp;rft.volume=287&amp;rft.issue=5461&amp;rft.pages=2196%E2%80%93204&amp;rft_id=info:pmid/10731133&amp;rft_id=http%3A%2F%2Fwww.sciencemag.org%2Fcgi%2Fpmidlookup%3Fview%3Dlong%26pmid%3D10731133&amp;rfr_id=info:sid/en.wikipedia.org:Sequence_assembly"><span style="display: none">&nbsp;</span></span> </span></li></div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l318" >Line 318:</td> <td colspan="2" class="diff-lineno">Line 318:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     <li id="cite_note-3"><span style="font-size: small"><b><a href="#cite_ref-3"><font color="#0645ad">^</font></a></b></span><span style="font-size: small"> Copy in Google groups of the </span><span style="font-size: small"><a class="external text" rel="nofollow" href="http://groups.google.com/group/bionet.software/browse_thread/thread/b34b348011d04f0e?fwc=1"><font color="#3366bb">post announcing MIRA 2.9.8 hybrid version</font></a></span><span style="font-size: small"> in the bionet.software Usenet group </span></li></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     <li id="cite_note-3"><span style="font-size: small"><b><a href="#cite_ref-3"><font color="#0645ad">^</font></a></b></span><span style="font-size: small"> Copy in Google groups of the </span><span style="font-size: small"><a class="external text" rel="nofollow" href="http://groups.google.com/group/bionet.software/browse_thread/thread/b34b348011d04f0e?fwc=1"><font color="#3366bb">post announcing MIRA 2.9.8 hybrid version</font></a></span><span style="font-size: small"> in the bionet.software Usenet group </span></li></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     <li id="cite_note-4"><span style="font-size: small"><b><a href="#cite_ref-4"><font color="#0645ad">^</font></a></b></span><span style="font-size: small"> <span class="citation Journal">Dohm JC, Lottaz C, Borodina T, Himmelbauer H (November 2007). </span></span><span class="citation Journal"><span style="font-size: small"><a class="external text" rel="nofollow" href="http://www.genome.org/cgi/pmidlookup?view=long&amp;pmid=17908823"><font color="#3366bb">&quot;SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing&quot;</font></a></span><span style="font-size: small">. <i>Genome Res.</i> <b>17</b> (11): 1697&ndash;706. </span><span style="font-size: small"><a title="Digital object identifier" href="/wiki/Digital_object_identifier"><font color="#0645ad">doi</font></a></span><span style="font-size: small">:</span><span style="font-size: small"><a class="external text" rel="nofollow" href="http://dx.doi.org/10.1101%2Fgr.6435207"><font color="#3366bb">10.1101/gr.6435207</font></a></span><span style="font-size: small">. </span><span style="font-size: small"><a class="mw-redirect" title="PubMed Identifier" href="/wiki/PubMed_Identifier"><font color="#0645ad">PMID</font></a></span><span style="font-size: small">&nbsp;</span><span style="font-size: small"><a class="external text" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/pubmed/17908823"><font color="#3366bb">17908823</font></a></span><span style="font-size: small">. </span><span style="font-size: small"><a title="PubMed Central" href="/wiki/PubMed_Central"><font color="#0645ad">PMC</font></a></span><span style="font-size: small">&nbsp;</span><span style="font-size: small"><a class="external text" rel="nofollow" href="http://www.pubmedcentral.gov/articlerender.fcgi?tool=pmcentrez&amp;artid=2045152"><font color="#3366bb">2045152</font></a></span><span style="font-size: small"><span class="printonly">. </span></span></span><span style="font-size: large"><span class="citation Journal"><span class="printonly"><a class="external free" rel="nofollow" href="http://www.genome.org/cgi/pmidlookup?view=long&amp;pmid=17908823"><span style="font-size: small"><font color="#3366bb">http://www.genome.org/cgi/pmidlookup?view=long&amp;pmid=17908823</font></span></a></span></span></span><span style="font-size: small"><span class="citation Journal">.</span><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=SHARCGS%2C+a+fast+and+highly+accurate+short-read+assembly+algorithm+for+de+novo+genomic+sequencing&amp;rft.jtitle=Genome+Res.&amp;rft.aulast=Dohm+JC%2C+Lottaz+C%2C+Borodina+T%2C+Himmelbauer+H&amp;rft.au=Dohm+JC%2C+Lottaz+C%2C+Borodina+T%2C+Himmelbauer+H&amp;rft.date=November+2007&amp;rft.volume=17&amp;rft.issue=11&amp;rft.pages=1697%E2%80%93706&amp;rft_id=info:doi/10.1101%2Fgr.6435207&amp;rft_id=info:pmid/17908823&amp;rft_id=http%3A%2F%2Fwww.genome.org%2Fcgi%2Fpmidlookup%3Fview%3Dlong%26pmid%3D17908823&amp;rfr_id=info:sid/en.wikipedia.org:Sequence_assembly"><span style="display: none">&nbsp;</span></span> </span></li></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     <li id="cite_note-4"><span style="font-size: small"><b><a href="#cite_ref-4"><font color="#0645ad">^</font></a></b></span><span style="font-size: small"> <span class="citation Journal">Dohm JC, Lottaz C, Borodina T, Himmelbauer H (November 2007). </span></span><span class="citation Journal"><span style="font-size: small"><a class="external text" rel="nofollow" href="http://www.genome.org/cgi/pmidlookup?view=long&amp;pmid=17908823"><font color="#3366bb">&quot;SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing&quot;</font></a></span><span style="font-size: small">. <i>Genome Res.</i> <b>17</b> (11): 1697&ndash;706. </span><span style="font-size: small"><a title="Digital object identifier" href="/wiki/Digital_object_identifier"><font color="#0645ad">doi</font></a></span><span style="font-size: small">:</span><span style="font-size: small"><a class="external text" rel="nofollow" href="http://dx.doi.org/10.1101%2Fgr.6435207"><font color="#3366bb">10.1101/gr.6435207</font></a></span><span style="font-size: small">. </span><span style="font-size: small"><a class="mw-redirect" title="PubMed Identifier" href="/wiki/PubMed_Identifier"><font color="#0645ad">PMID</font></a></span><span style="font-size: small">&nbsp;</span><span style="font-size: small"><a class="external text" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/pubmed/17908823"><font color="#3366bb">17908823</font></a></span><span style="font-size: small">. </span><span style="font-size: small"><a title="PubMed Central" href="/wiki/PubMed_Central"><font color="#0645ad">PMC</font></a></span><span style="font-size: small">&nbsp;</span><span style="font-size: small"><a class="external text" rel="nofollow" href="http://www.pubmedcentral.gov/articlerender.fcgi?tool=pmcentrez&amp;artid=2045152"><font color="#3366bb">2045152</font></a></span><span style="font-size: small"><span class="printonly">. </span></span></span><span style="font-size: large"><span class="citation Journal"><span class="printonly"><a class="external free" rel="nofollow" href="http://www.genome.org/cgi/pmidlookup?view=long&amp;pmid=17908823"><span style="font-size: small"><font color="#3366bb">http://www.genome.org/cgi/pmidlookup?view=long&amp;pmid=17908823</font></span></a></span></span></span><span style="font-size: small"><span class="citation Journal">.</span><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=SHARCGS%2C+a+fast+and+highly+accurate+short-read+assembly+algorithm+for+de+novo+genomic+sequencing&amp;rft.jtitle=Genome+Res.&amp;rft.aulast=Dohm+JC%2C+Lottaz+C%2C+Borodina+T%2C+Himmelbauer+H&amp;rft.au=Dohm+JC%2C+Lottaz+C%2C+Borodina+T%2C+Himmelbauer+H&amp;rft.date=November+2007&amp;rft.volume=17&amp;rft.issue=11&amp;rft.pages=1697%E2%80%93706&amp;rft_id=info:doi/10.1101%2Fgr.6435207&amp;rft_id=info:pmid/17908823&amp;rft_id=http%3A%2F%2Fwww.genome.org%2Fcgi%2Fpmidlookup%3Fview%3Dlong%26pmid%3D17908823&amp;rfr_id=info:sid/en.wikipedia.org:Sequence_assembly"><span style="display: none">&nbsp;</span></span> </span></li></div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>     <li id="cite_note-5"><span style="font-size: small"><b><a href="#cite_ref-5"><font color="#0645ad">^</font></a></b></span><span style="font-size: medium"><a class="external text" rel="nofollow" href="http://seqanswers.com/forums/showthread.php?t=43"><span style="font-size: small"><font color="#3366bb">list of software including mapping assemblers in the SeqAnswers discussion forum.</font></span></a></span<del class="diffchange diffchange-inline">><a class="external text" rel="nofollow" href="http://seqanswers.com/forums/showthread.php?t=43"></a</del>></li></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>     <li id="cite_note-5"><span style="font-size: small"><b><a href="#cite_ref-5"><font color="#0645ad">^</font></a></b></span><span style="font-size: medium"><a class="external text" rel="nofollow" href="http://seqanswers.com/forums/showthread.php?t=43"><span style="font-size: small"><font color="#3366bb">list of software including mapping assemblers in the SeqAnswers discussion forum.</font></span></a></span></li></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     <li id="cite_note-6"><span style="font-size: small"><b><a href="#cite_ref-6"><font color="#0645ad">^</font></a></b></span><span style="font-size: small"> <span class="citation Journal">Boisvert S, Laviolette F, Corbeil J. (October 2010). </span></span><span class="citation Journal"><span style="font-size: small"><a class="external text" rel="nofollow" href="http://www.liebertonline.com/doi/abs/10.1089/cmb.2009.0238"><font color="#3366bb">&quot;Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies.&quot;</font></a></span><span style="font-size: small">. <i>J Comput Biol.</i> <b>17</b> (11): 1519-33. </span><span style="font-size: small"><a title="Digital object identifier" href="/wiki/Digital_object_identifier"><font color="#0645ad">doi</font></a></span><span style="font-size: small">:</span><span style="font-size: small"><a class="external text" rel="nofollow" href="http://dx.doi.org/10.1089%2Fcmb.2009.0238"><font color="#3366bb">10.1089/cmb.2009.0238</font></a></span><span style="font-size: small">. </span><span style="font-size: small"><a class="mw-redirect" title="PubMed Identifier" href="/wiki/PubMed_Identifier"><font color="#0645ad">PMID</font></a></span><span style="font-size: small">&nbsp;</span><span style="font-size: small"><a class="external text" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/pubmed/20958248"><font color="#3366bb">20958248</font></a></span><span style="font-size: small"><span class="printonly">. </span></span></span><span style="font-size: large"><span class="citation Journal"><span class="printonly"><a class="external free" rel="nofollow" href="http://www.liebertonline.com/doi/abs/10.1089/cmb.2009.0238"><span style="font-size: small"><font color="#3366bb">http://www.liebertonline.com/doi/abs/10.1089/cmb.2009.0238</font></span></a></span></span></span><span style="font-size: small"><span class="citation Journal">.</span> </span></li></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     <li id="cite_note-6"><span style="font-size: small"><b><a href="#cite_ref-6"><font color="#0645ad">^</font></a></b></span><span style="font-size: small"> <span class="citation Journal">Boisvert S, Laviolette F, Corbeil J. (October 2010). </span></span><span class="citation Journal"><span style="font-size: small"><a class="external text" rel="nofollow" href="http://www.liebertonline.com/doi/abs/10.1089/cmb.2009.0238"><font color="#3366bb">&quot;Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies.&quot;</font></a></span><span style="font-size: small">. <i>J Comput Biol.</i> <b>17</b> (11): 1519-33. </span><span style="font-size: small"><a title="Digital object identifier" href="/wiki/Digital_object_identifier"><font color="#0645ad">doi</font></a></span><span style="font-size: small">:</span><span style="font-size: small"><a class="external text" rel="nofollow" href="http://dx.doi.org/10.1089%2Fcmb.2009.0238"><font color="#3366bb">10.1089/cmb.2009.0238</font></a></span><span style="font-size: small">. </span><span style="font-size: small"><a class="mw-redirect" title="PubMed Identifier" href="/wiki/PubMed_Identifier"><font color="#0645ad">PMID</font></a></span><span style="font-size: small">&nbsp;</span><span style="font-size: small"><a class="external text" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/pubmed/20958248"><font color="#3366bb">20958248</font></a></span><span style="font-size: small"><span class="printonly">. </span></span></span><span style="font-size: large"><span class="citation Journal"><span class="printonly"><a class="external free" rel="nofollow" href="http://www.liebertonline.com/doi/abs/10.1089/cmb.2009.0238"><span style="font-size: small"><font color="#3366bb">http://www.liebertonline.com/doi/abs/10.1089/cmb.2009.0238</font></span></a></span></span></span><span style="font-size: small"><span class="citation Journal">.</span> </span></li></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></ol></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></ol></div></td></tr>  </table>

WikiSysop http://pgi.re.kr/index.php?title=Sequence_assembly&diff=3347&oldid=prev WikiSysop at 15:09, 18 December 2010 2010-12-18T15:09:33Z

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WikiSysop http://pgi.re.kr/index.php?title=Sequence_assembly&diff=3346&oldid=prev WikiSysop: Created page with "<p><span style="color: #000000">In bioinformatics, <b>sequence assembly</b> refers to aligning and merging fragments of a much longer DNA sequence in order to reconstruct the ori..." 2010-12-18T14:58:06Z

<p>Created page with "<p><span style="color: #000000">In bioinformatics, <b>sequence assembly</b> refers to aligning and merging fragments of a much longer DNA sequence in order to reconstruct the ori..."</p> <a href="http://pgi.re.kr/index.php?title=Sequence_assembly&diff=3346">Show changes</a>

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