Bowtie is a software package commonly used for
sequence alignment
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Alig ...
and
sequence analysis in
bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...
.
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.
Bowtie is
open-source software and is currently maintained by
Johns Hopkins University.
History
The Bowtie sequence aligner was originally developed by
Ben Langmead
Ben Langmead is a computational biologist and associate professor in the Computational Biology & Medicine Group at Johns Hopkins University.
Education
Langmead gained his Bachelor of Arts degree in computer science from Columbia College, Columbi ...
''et al.'' at the
University of Maryland in 2009.
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);
a similar method is used by the BWA
and
SOAP2 alignment methods.
Bowtie conducts a quality-aware, greedy, randomized,
depth-first search
Depth-first search (DFS) is an algorithm for traversing or searching tree or graph data structures. The algorithm starts at the root node (selecting some arbitrary node as the root node in the case of a graph) and explores as far as possible alon ...
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
A top hat (also called a high hat, a cylinder hat, or, informally, a topper) is a tall, flat-crowned hat for men traditionally associated with formal wear in Western dress codes, meaning white tie, morning dress, or frock coat. Traditionally m ...
,
Cufflinks
and the CummeRbund
Bioconductor package.
Bowtie 2
On 16 October 2011, the developers released a beta
fork of the project called Bowtie 2.
In addition to the Burrows-Wheeler transform, Bowtie 2 also uses an
FM-index (similar to a
suffix array
In computer science, a suffix array is a sorted array of all suffixes of a string. It is a data structure used in, among others, full-text indices, data-compression algorithms, and the field of bibliometrics.
Suffix arrays were introduced by as ...
) 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 SourceForgeBowtie 2 page on SourceForge
{{Bioinformatics
Bioinformatics algorithms
Bioinformatics software
Laboratory software
Software using the Artistic license