Skip to main content

Multiple Sequence Alignment Computation Using the T-Coffee Regressive Algorithm Implementation

  • Protocol
  • First Online:
Multiple Sequence Alignment

Abstract

Many fields of biology rely on the inference of accurate multiple sequence alignments (MSA) of biological sequences. Unfortunately, the problem of assembling an MSA is NP-complete thus limiting computation to approximate solutions using heuristics solutions. The progressive algorithm is one of the most popular frameworks for the computation of MSAs. It involves pre-clustering the sequences and aligning them starting with the most similar ones. The scalability of this framework is limited, especially with respect to accuracy. We present here an alternative approach named regressive algorithm. In this framework, sequences are first clustered and then aligned starting with the most distantly related ones. This approach has been shown to greatly improve accuracy during scale-up, especially on datasets featuring 10,000 sequences or more. Another benefit is the possibility to integrate third-party clustering methods and third-party MSA aligners. The regressive algorithm has been tested on up to 1.5 million sequences, its implementation is available in the T-Coffee package.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 99.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 129.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Hogeweg P, Hesper B (1984) The alignment of sets of sequences and the construction of phyletic trees: an integrated method. J Mol Evol 20:175–186. https://doi.org/10.1007/bf02257378

    Article  CAS  PubMed  Google Scholar 

  2. Garriga E, Di Tommaso P, Magis C et al (2019) Large multiple sequence alignments with a root-to-leaf regressive method. Nat Biotechnol 37(12):1466–1470

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Sievers F, Wilm A, Dineen D et al (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal omega. Mol Syst Biol 7:539. https://doi.org/10.1038/msb.2011.75

    Article  PubMed  PubMed Central  Google Scholar 

  4. Finn RD, Bateman A, Clements J et al (2014) Pfam: the protein families database. Nucleic Acids Res 42:D222–D230. https://doi.org/10.1093/nar/gkt1223

    Article  CAS  PubMed  Google Scholar 

  5. Notredame C, Higgins DG, Heringa J (2000) T-coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 302:205–217. https://doi.org/10.1006/jmbi.2000.4042

    Article  CAS  PubMed  Google Scholar 

  6. Blackshields G, Sievers F, Shi W et al (2010) Sequence embedding for fast construction of guide trees for multiple sequence alignment. Algorithms Mol Biol 5:21. https://doi.org/10.1186/1748-7188-5-21

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Katoh K, Toh H (2007) PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences. Bioinformatics 23:372–374. https://doi.org/10.1093/bioinformatics/btl592

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

We acknowledge Des Higgins and Olivier Gascuel for useful discussions and feedback.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Cedric Notredame .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Garriga, E. et al. (2021). Multiple Sequence Alignment Computation Using the T-Coffee Regressive Algorithm Implementation. In: Katoh, K. (eds) Multiple Sequence Alignment. Methods in Molecular Biology, vol 2231. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1036-7_6

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-1036-7_6

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1035-0

  • Online ISBN: 978-1-0716-1036-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics