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Bowtie (sequence analysis)
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<h2 id="history">History</h2> <p>The Bowtie sequence aligner was originally developed by <a href="/facts/Ben_Langmead/A6RLIQCJ">Ben Langmead</a> <i>et al.</i> at the <a href="/facts/University_of_Maryland/Wmc5R1kM">University of Maryland</a> in 2009.<a class="footnote-ref" id="fnref:3" href="#fn:3"><sup>3</sup></a> The aligner is typically used with short reads and a large <a href="/facts/Reference_genome/0N144oyY">reference genome</a>, or for <a href="/facts/Whole_genome_sequencing/WNuHaU2K">whole genome analysis</a>. Bowtie is promoted as "an ultrafast, memory-efficient short aligner for short <a href="/facts/DNA/nB89Iauz">DNA</a> sequences." The speed increase of Bowtie is partly due to implementing the <a href="/facts/Burrows%25E2%2580%2593Wheeler_transform/yxIc9E94">Burrows–Wheeler transform</a> for aligning,<a class="footnote-ref" id="fnref:4" href="#fn:4"><sup>4</sup></a> which reduces the <a href="/facts/Memory_footprint/wnS6TgpY">memory footprint</a> (typically to around 2.2GB for the human genome);<a class="footnote-ref" id="fnref:5" href="#fn:5"><sup>5</sup></a> a similar method is used by the BWA<a class="footnote-ref" id="fnref:6" href="#fn:6"><sup>6</sup></a> and <a href="/facts/Short_Oligonucleotide_Analysis_Package/bzFYAN1h">SOAP2</a><a class="footnote-ref" id="fnref:7" href="#fn:7"><sup>7</sup></a> alignment methods.<a class="footnote-ref" id="fnref:8" href="#fn:8"><sup>8</sup></a> </p><p>Bowtie conducts a quality-aware, greedy, randomized, <a href="/facts/Depth-first_search/luxJKVph">depth-first search</a> through the space of possible alignments. Because the search is greedy, the first valid alignment encountered by Bowtie will not necessarily be the 'best' in terms of the number of mismatches or in terms of quality. </p><p>Bowtie is used as a sequence aligner by a number of other related bioinformatics algorithms, including <a href="/facts/TopHat_(bioinformatics)/su5cDMkf">TopHat</a>,<a class="footnote-ref" id="fnref:9" href="#fn:9"><sup>9</sup></a> Cufflinks<a class="footnote-ref" id="fnref:10" href="#fn:10"><sup>10</sup></a> and the CummeRbund <a href="/facts/Bioconductor/SQyvk4TM">Bioconductor</a> package.<a class="footnote-ref" id="fnref:11" href="#fn:11"><sup>11</sup></a> </p> <h2 id="bowtie-2">Bowtie 2</h2> <p>On 16 October 2011, the developers released a beta <a href="/facts/Fork_(software_development)/D6khxhpr">fork</a> of the project called Bowtie 2.<a class="footnote-ref" id="fnref:12" href="#fn:12"><sup>12</sup></a> In addition to the Burrows-Wheeler transform, Bowtie 2 also uses an <a href="/facts/FM-index/USSL4YMU">FM-index</a> (similar to a <a href="/facts/Suffix_array/Q87p7bYH">suffix array</a>) to keep its memory footprint small. Due to its implementation, Bowtie 2 is more suited to finding longer, gapped alignments in comparison with the original Bowtie method. There is no upper limit on read length in Bowtie 2 and it allows alignments to overlap ambiguous characters in the reference. </p> <h2 id="external-links">External links</h2> <ul><li><a href="http://bowtie-bio.sourceforge.net/index.shtml">Bowtie page on SourceForge</a></li> <li><a href="http://bowtie-bio.sourceforge.net/bowtie2/index.shtml">Bowtie 2 page on SourceForge</a></li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>Langmead, Ben; Cole Trapnell; Mihai Pop; Steven L Salzberg (4 March 2009). "Ultrafast and memory-efficient alignment of short DNA sequences to the human genome". Genome Biology. 10 (3): 10:R25. doi:10.1186/gb-2009-10-3-r25. PMC 2690996. PMID 19261174. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690996" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690996</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>Langmead, Ben; Cole Trapnell; Mihai Pop; Steven L Salzberg (4 March 2009). "Ultrafast and memory-efficient alignment of short DNA sequences to the human genome". Genome Biology. 10 (3): 10:R25. doi:10.1186/gb-2009-10-3-r25. PMC 2690996. PMID 19261174. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690996" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690996</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>Langmead, Ben; Cole Trapnell; Mihai Pop; Steven L Salzberg (4 March 2009). "Ultrafast and memory-efficient alignment of short DNA sequences to the human genome". Genome Biology. 10 (3): 10:R25. doi:10.1186/gb-2009-10-3-r25. PMC 2690996. PMID 19261174. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690996" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690996</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>Ferragina, Paolo; Manzini, Giovanni (2005). "Indexing compressed text". Journal of the ACM. 52 (4): 552–581. doi:10.1145/1082036.1082039. S2CID 6200428. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>"Bowtie: An ultrafast, memory-efficient short read aligner - SourceForge". Retrieved 29 November 2013. <a href="http://bowtie-bio.sourceforge.net/index.shtml" target="_blank">http://bowtie-bio.sourceforge.net/index.shtml</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>Li, H.; Durbin, R. (18 May 2009). "Fast and accurate short read alignment with Burrows-Wheeler transform". Bioinformatics. 25 (14): 1754–1760. doi:10.1093/bioinformatics/btp324. PMC 2705234. PMID 19451168. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705234" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705234</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>Li, R.; Yu, C.; Li, Y.; Lam, T.-W.; Yiu, S.-M.; Kristiansen, K.; Wang, J. (3 June 2009). "SOAP2: an improved ultrafast tool for short read alignment". Bioinformatics. 25 (15): 1966–1967. doi:10.1093/bioinformatics/btp336. PMID 19497933. <a href="https://doi.org/10.1093%2Fbioinformatics%2Fbtp336" target="_blank">https://doi.org/10.1093%2Fbioinformatics%2Fbtp336</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>"Bowtie: An ultrafast, memory-efficient short read aligner - SourceForge". Retrieved 29 November 2013. <a href="http://bowtie-bio.sourceforge.net/index.shtml" target="_blank">http://bowtie-bio.sourceforge.net/index.shtml</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li> <li id="fn:9"><p>Trapnell, C.; Pachter, L.; Salzberg, S. L. (16 March 2009). "TopHat: discovering splice junctions with RNA-Seq". Bioinformatics. 25 (9): 1105–1111. doi:10.1093/bioinformatics/btp120. PMC 2672628. PMID 19289445. <a href="/wiki/Lior_Pachter" target="_blank">/wiki/Lior_Pachter</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li> <li id="fn:10"><p>Trapnell, Cole; Roberts, Adam; Goff, Loyal; Pertea, Geo; Kim, Daehwan; Kelley, David R; Pimentel, Harold; Salzberg, Steven L; Rinn, John L; Pachter, Lior (1 March 2012). "Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks". Nature Protocols. 7 (3): 562–578. doi:10.1038/nprot.2012.016. PMC 3334321. PMID 22383036. <a href="/wiki/Lior_Pachter" target="_blank">/wiki/Lior_Pachter</a> <a href="#fnref:10" class="footnote-back-ref">↩</a></p></li> <li id="fn:11"><p>"CummeRbund - An R package for persistent storage, analysis, and visualization of RNA-Seq from cufflinks output". Retrieved 11 August 2015. <a href="http://compbio.mit.edu/cummeRbund/" target="_blank">http://compbio.mit.edu/cummeRbund/</a> <a href="#fnref:11" class="footnote-back-ref">↩</a></p></li> <li id="fn:12"><p>Langmead, Ben; Salzberg, Steven L (4 March 2012). "Fast gapped-read alignment with Bowtie 2". Nature Methods. 9 (4): 357–359. doi:10.1038/nmeth.1923. PMC 3322381. PMID 22388286. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322381" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322381</a> <a href="#fnref:12" class="footnote-back-ref">↩</a></p></li> </ol>