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Multiple Sequence Alignment Methods

Overview of attention for book
Cover of 'Multiple Sequence Alignment Methods'

Table of Contents

  1. Altmetric Badge
    Book Overview
  2. Altmetric Badge
    Chapter 1 Dynamic Programming
  3. Altmetric Badge
    Chapter 2 Heuristic Alignment Methods
  4. Altmetric Badge
    Chapter 3 Objective Functions
  5. Altmetric Badge
    Chapter 4 Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment.
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    Chapter 5 BLAST and FASTA Similarity Searching for Multiple Sequence Alignment
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    Chapter 6 Multiple Sequence Alignment Methods
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    Chapter 7 T-coffee: tree-based consistency objective function for alignment evaluation.
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    Chapter 8 MAFFT: Iterative Refinement and Additional Methods
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    Chapter 9 Multiple Sequence Alignment Methods
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    Chapter 10 Phylogeny-aware alignment with PRANK.
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    Chapter 11 GramAlign: Fast alignment driven by grammar-based phylogeny
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    Chapter 12 Multiple Sequence Alignment with DIALIGN
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    Chapter 13 PicXAA: A Probabilistic Scheme for Finding the Maximum Expected Accuracy Alignment of Multiple Biological Sequences
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    Chapter 14 Multiple Protein Sequence Alignment with MSAProbs
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    Chapter 15 Large-Scale Multiple Sequence Alignment and Tree Estimation Using SATé
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    Chapter 16 PRALINE: A Versatile Multiple Sequence Alignment Toolkit
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    Chapter 17 PROMALS3D: Multiple Protein Sequence Alignment Enhanced with Evolutionary and Three-Dimensional Structural Information
  19. Altmetric Badge
    Chapter 18 MSACompro: Improving Multiple Protein Sequence Alignment by Predicted Structural Features
Attention for Chapter 4: Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment.
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About this Attention Score

  • In the top 5% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (96th percentile)
  • High Attention Score compared to outputs of the same age and source (98th percentile)

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2 blogs
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28 X users
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1 peer review site
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2 Wikipedia pages

Citations

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72 Mendeley
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Chapter title
Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment.
Chapter number 4
Book title
Multiple Sequence Alignment Methods
Published in
Methods in molecular biology, January 2014
DOI 10.1007/978-1-62703-646-7_4
Pubmed ID
Book ISBNs
978-1-62703-645-0, 978-1-62703-646-7
Authors

Stefano Iantorno, Kevin Gori, Nick Goldman, Manuel Gil, Christophe Dessimoz, Iantorno, Stefano, Gori, Kevin, Goldman, Nick, Gil, Manuel, Dessimoz, Christophe

Abstract

Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult to assess in those analyses. To compare the performance of different aligners and help detect systematic errors in alignments, a number of benchmarking strategies have been pursued. Here we present an overview of the main strategies-based on simulation, consistency, protein structure, and phylogeny-and discuss their different advantages and associated risks. We outline a set of desirable characteristics for effective benchmarking, and evaluate each strategy in light of them. We conclude that there is currently no universally applicable means of benchmarking MSA, and that developers and users of alignment tools should base their choice of benchmark depending on the context of application-with a keen awareness of the assumptions underlying each benchmarking strategy.

X Demographics

X Demographics

The data shown below were collected from the profiles of 28 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 72 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 2 3%
Spain 2 3%
Germany 2 3%
Sweden 1 1%
Unknown 65 90%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 23 32%
Student > Master 15 21%
Researcher 11 15%
Student > Bachelor 4 6%
Student > Postgraduate 4 6%
Other 7 10%
Unknown 8 11%
Readers by discipline Count As %
Agricultural and Biological Sciences 33 46%
Biochemistry, Genetics and Molecular Biology 15 21%
Computer Science 10 14%
Medicine and Dentistry 3 4%
Arts and Humanities 1 1%
Other 3 4%
Unknown 7 10%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 34. 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 23 August 2020.
All research outputs
#1,133,112
of 24,877,869 outputs
Outputs from Methods in molecular biology
#109
of 13,978 outputs
Outputs of similar age
#12,519
of 317,860 outputs
Outputs of similar age from Methods in molecular biology
#7
of 565 outputs
Altmetric has tracked 24,877,869 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 95th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 13,978 research outputs from this source. They receive a mean Attention Score of 3.5. This one has done particularly well, scoring higher than 99% 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 317,860 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 96% of its contemporaries.
We're also able to compare this research output to 565 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 98% of its contemporaries.