Bowtie is a software package commonly used for sequence alignment and

sequence analysis In bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution. Methodologies used include sequence alig ...

in bioinformatics. The source code for the package is distributed freely and compiled binaries are available for

Linux Linux ( or ) is a family of open-source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically packaged as a Linux distribution, w ...

macOS macOS (; previously OS X and originally Mac OS X) is a Unix operating system developed and marketed by Apple Inc. since 2001. It is the primary operating system for Apple's Mac computers. Within the market of desktop and lapt ...

and

Windows Windows is a group of several proprietary graphical operating system families developed and marketed by Microsoft. Each family caters to a certain sector of the computing industry. For example, Windows NT for consumers, Windows Server for ser ...

platforms. As of 2017, the ''

Genome Biology ''Genome Biology'' is a peer-reviewed open access scientific journal covering research in genomics. It was established in 2000 and is published by BioMed Central. The chief editor is currently Andrew Cosgrove (BioMed Central, New York). Abstractin ...

'' paper describing the original Bowtie method has been cited more than 11,000 times. Bowtie is

open-source software Open-source software (OSS) is computer software that is released under a license in which the copyright holder grants users the rights to use, study, change, and distribute the software and its source code to anyone and for any purpose. Op ...

and is currently maintained by

Johns Hopkins University Johns Hopkins University (Johns Hopkins, Hopkins, or JHU) is a private research university in Baltimore, Maryland. Founded in 1876, Johns Hopkins is the oldest research university in the United States and in the western hemisphere. It consi ...

History

The Bowtie sequence aligner was originally developed by Ben Langmead ''et al.'' at the

University of Maryland The University of Maryland, College Park (University of Maryland, UMD, or simply Maryland) is a public land-grant research university in College Park, Maryland. Founded in 1856, UMD is the flagship institution of the University System of M ...

in 2009. The aligner is typically used with short reads and a large

reference genome A reference genome (also known as a reference assembly) is a digital nucleic acid sequence database, assembled by scientists as a representative example of the set of genes in one idealized individual organism of a species. As they are assemble ...

, 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 The Burrows–Wheeler transform (BWT, also called block-sorting compression) rearranges a character string into runs of similar characters. This is useful for compression, since it tends to be easy to compress a string that has runs of repeated c ...

for aligning, which reduces the

memory footprint Memory footprint refers to the amount of main memory that a program uses or references while running. The word footprint generally refers to the extent of physical dimensions that an object occupies, giving a sense of its size. In computing, the ...

(typically to around 2.2GB for the human genome); a similar method is used by the BWA and SOAP2 alignment methods. 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, Cufflinks and the CummeRbund

Bioconductor Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology. Bioconductor is based primarily on the statistical R programm ...

package.

Bowtie 2

On 16 October 2011, the developers released a beta

fork In cutlery or kitchenware, a fork (from la, furca 'pitchfork') is a utensil, now usually made of metal, whose long handle terminates in a head that branches into several narrow and often slightly curved tine (structural), tines with which one ...

of the project called Bowtie 2. In addition to the Burrows-Wheeler transform, Bowtie 2 also uses an

FM-index In computer science, an FM-index is a compressed full-text substring index based on the Burrows–Wheeler transform, with some similarities to the suffix array. It was created by Paolo Ferragina and Giovanni Manzini,Paolo Ferragina and Giovanni Manz ...

(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.

References

External links

Bowtie page on SourceForge

Bowtie 2 page on SourceForge
{{Bioinformatics Bioinformatics algorithms Bioinformatics software Laboratory software Software using the Artistic license