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FAMSA: Fast and accurate multiple sequence alignment of huge protein families

Overview of attention for article published in Scientific Reports, September 2016
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (82nd percentile)
  • Good Attention Score compared to outputs of the same age and source (77th percentile)

Mentioned by

twitter
20 tweeters

Citations

dimensions_citation
22 Dimensions

Readers on

mendeley
58 Mendeley
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Title
FAMSA: Fast and accurate multiple sequence alignment of huge protein families
Published in
Scientific Reports, September 2016
DOI 10.1038/srep33964
Pubmed ID
Authors

Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Adam Gudyś

Abstract

Rapid development of modern sequencing platforms has contributed to the unprecedented growth of protein families databases. The abundance of sets containing hundreds of thousands of sequences is a formidable challenge for multiple sequence alignment algorithms. The article introduces FAMSA, a new progressive algorithm designed for fast and accurate alignment of thousands of protein sequences. Its features include the utilization of the longest common subsequence measure for determining pairwise similarities, a novel method of evaluating gap costs, and a new iterative refinement scheme. What matters is that its implementation is highly optimized and parallelized to make the most of modern computer platforms. Thanks to the above, quality indicators, i.e. sum-of-pairs and total-column scores, show FAMSA to be superior to competing algorithms, such as Clustal Omega or MAFFT for datasets exceeding a few thousand sequences. Quality does not compromise on time or memory requirements, which are an order of magnitude lower than those in the existing solutions. For example, a family of 415519 sequences was analyzed in less than two hours and required no more than 8 GB of RAM. FAMSA is available for free at http://sun.aei.polsl.pl/REFRESH/famsa.

Twitter Demographics

The data shown below were collected from the profiles of 20 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 58 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 1 2%
Spain 1 2%
Argentina 1 2%
Unknown 55 95%

Demographic breakdown

Readers by professional status Count As %
Researcher 14 24%
Student > Ph. D. Student 13 22%
Student > Master 5 9%
Student > Bachelor 4 7%
Student > Postgraduate 3 5%
Other 8 14%
Unknown 11 19%
Readers by discipline Count As %
Agricultural and Biological Sciences 14 24%
Biochemistry, Genetics and Molecular Biology 13 22%
Computer Science 10 17%
Earth and Planetary Sciences 1 2%
Arts and Humanities 1 2%
Other 5 9%
Unknown 14 24%

Attention Score in Context

This research output has an Altmetric Attention Score of 10. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 29 October 2019.
All research outputs
#2,133,169
of 16,109,433 outputs
Outputs from Scientific Reports
#18,084
of 84,958 outputs
Outputs of similar age
#66,877
of 392,275 outputs
Outputs of similar age from Scientific Reports
#1,071
of 4,749 outputs
Altmetric has tracked 16,109,433 research outputs across all sources so far. Compared to these this one has done well and is in the 86th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 84,958 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 16.2. This one has done well, scoring higher than 78% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 392,275 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 82% of its contemporaries.
We're also able to compare this research output to 4,749 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 77% of its contemporaries.