To install click the Add extension button. That's it.

The source code for the WIKI 2 extension is being checked by specialists of the Mozilla Foundation, Google, and Apple. You could also do it yourself at any point in time.

Kelly Slayton
Congratulations on this excellent venture… what a great idea!
Alexander Grigorievskiy
I use WIKI 2 every day and almost forgot how the original Wikipedia looks like.
Live Statistics
English Articles
Improved in 24 Hours
Added in 24 Hours
Show all languages
What we do. Every page goes through several hundred of perfecting techniques; in live mode. Quite the same Wikipedia. Just better.

Bowtie (sequence analysis)

From Wikipedia, the free encyclopedia

Original author(s) Ben Langmead,Cole Trapnell, Mihai Pop and Steven Salzberg
Developer(s) Ben Langmead et al.,
Stable release
2.3.4 / 29 December 2017; 2 days ago (2017-12-29)
Development status Active
Operating system Linux, macOS, Windows
Size 14.7 MB (Source)
Type Bioinformatics

Bowtie is a software package commonly used for sequence alignment and sequence analysis in bioinformatics.[1].The source code for the package is distributed freely and compiled binaries are available for Linux, macOS and Windows platforms. As of 2017, the Genome Biology paper describing the original Bowtie method has been cited more than 11,000 times.[1] Bowtie is open-source software and is currently maintained by Johns Hopkins University.

YouTube Encyclopedic

  • 1/3
    6 309
    33 743
    4 060
  • How to Align Sequences Webinar (6/7) High-throughput Sequence Alignment
  • 4) Next Generation Sequencing (NGS) - Data Analysis
  • 用 bowtie 做 mapping 的動作




The Bowtie sequence aligner was originally developed by Ben Langmead et al. at the University of Maryland in 2009.[1] The aligner is typically used with short reads and a large reference genome, or for whole genome analysis. Bowtie is promoted as "an ultrafast, memory-efficient short aligner for short DNA sequences." The speed increase of Bowtie is partly due to implementing the Burrows–Wheeler transform for aligning, which reduces the memory footprint (typically to around 2.2GB for the human genome);[2] a similar method is used by the BWA[3] and SOAP2[4] alignment methods. [2]

Bowtie conducts a quality-aware, greedy, randomized, depth-first search 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.

Bowtie is used as a sequence aligner by a number of other related bioinformatics algorithms, including TopHat,[5] Cufflinks[6] and the CummeRbund Bioconductor package.[7]

Bowtie 2

On 16 October 2011, the developers released a beta fork of the project called Bowtie 2.[8] In addition to the Burrows-Wheeler transform, Bowtie 2 also uses an FM-index (similar to a suffix array) 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.


  1. ^ a b c 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" (PDF). Genome Biology. 10 (3): 10:R25. doi:10.1186/gb-2009-10-3-r25. PMC 2690996Freely accessible. PMID 19261174. Retrieved 29 November 2013. 
  2. ^ a b "Bowtie: An ultrafast, memory-efficient short read aligner - SourceForge". Retrieved 29 November 2013. 
  3. ^ 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 2705234Freely accessible. PMID 19451168. 
  4. ^ 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. 
  5. ^ 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 2672628Freely accessible. PMID 19289445. 
  6. ^ "CummeRbund - An R package for persistent storage, analysis, and visualization of RNA-Seq from cufflinks output". Retrieved 11 August 2015. 
  7. ^ 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 3322381Freely accessible. PMID 22388286. 

External links

This page was last edited on 31 December 2017, at 11:58.
Basis of this page is in Wikipedia. Text is available under the CC BY-SA 3.0 Unported License. Non-text media are available under their specified licenses. Wikipedia® is a registered trademark of the Wikimedia Foundation, Inc. WIKI 2 is an independent company and has no affiliation with Wikimedia Foundation.