MUSCLE (software)

from Wikipedia, the free encyclopedia
MUSCLE
Basic data

developer Robert C. Edgar
Publishing year 2004
operating system Linux, macOS, Windows
programming language C ++
category Alignment
License public domain software
www.drive5.com/muscle

MUltiple Sequence Comparison by Log-Expectation (MUSCLE) is a computer program for processing alignments consisting of protein or nucleotide sequences and is accessible without a license. The method was published by Robert C. Edgar in two articles in 2004. The first article presented the algorithm for creating the alignment and was published in Nucleic Acids Research . The second article, published in BMC Bioinformatics, was more about the technical details.

algorithm

The MUSCLE algorithm is divided into three sections: the draft progressive , the improved progressive and the refinement section. In the first section, a first concept of the alignment is created, with speed being the focus here. In the second section, Kimura distances are used to obtain a more accurate alignment. In the final section, the alignment from section two is refined again. Multiple alignments are available after each section. In the first two sections of the algorithm, the time complexity and DSPACE are given as O ( N 2 L + NL 2 ) and O ( N 2 + NL + L 2 ). Another term is added in the final section: O ( N 3 L ). MUSCLE is often used instead of Clustal because it usually (but not always) provides better alignments. In addition, MUSCLE is significantly faster in creating the alignment, especially with larger alignments.

integration

MUSCLE is available in various programs, including DNASTAR's Lasergene, Geneious, MacVector, Sequencher, MEGA and UGENE, as a plug-in. MUSCLE is also available as a web service via the European Molecular Biology Laboratory (EMBL) and the European Bioinformatics Institute (EBI). The two articles describing MUSCLE were cited nearly 25,000 times (February 15, 2018).

See also

Individual evidence

  1. ↑ www.drive5.com . (accessed on March 13, 2018).
  2. ↑ Robert C. Edgar: MUSCLE: multiple sequence alignment with high accuracy and high throughput . In: Nucleic Acids Research . tape 32 , no. 5 , 2004, ISSN  0305-1048 , p. 1792–1797 , doi : 10.1093 / nar / gkh340 , PMID 15034147 , PMC 390337 (free full text).
  3. ↑ Robert C. Edgar: MUSCLE: a multiple sequence alignment method with reduced time and space complexity . In: BMC Bioinformatics . tape 5 , August 19, 2004, ISSN  1471-2105 , p. 113 , doi : 10.1186 / 1471-2105-5-113 , PMID 15318951 , PMC 517706 (free full text).