Protein Sequence Msa

references/citation.bib

@ARTICLE{Sievers2011,
  ABSTRACT = {Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high‐quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments. The accuracy of the package on smaller test cases is similar to that of the high‐quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam.},
  AUTHOR = {Sievers, Fabian and Wilm, Andreas and Dineen, David and Gibson, Toby J. and Karplus, Kevin and Li, Weizhong and Lopez, Rodrigo and McWilliam, Hamish and Remmert, Michael and Söding, Johannes and Thompson, Julie D. and Higgins, Desmond G.},
  URL = {https://doi.org/10.1038/msb.2011.75},
  DATE = {2011-10-11},
  DOI = {10.1038/msb.2011.75},
  ISSN = {1744-4292},
  JOURNALTITLE = {Molecular Systems Biology},
  NUMBER = {1},
  PAGES = {MSB201175},
  TITLE = {Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega},
  VOLUME = {7},
}

@ARTICLE{Goujon2010,
  ABSTRACT = {The EMBL-EBI provides access to various mainstream sequence analysis applications. These include sequence similarity search services such as BLAST, FASTA, InterProScan and multiple sequence alignment tools such as ClustalW, T-Coffee and MUSCLE. Through the sequence similarity search services, the users can search mainstream sequence databases such as EMBL-Bank and UniProt, and more than 2000 completed genomes and proteomes. We present here a new framework aimed at both novice as well as expert users that exposes novel methods of obtaining annotations and visualizing sequence analysis results through one uniform and consistent interface. These services are available over the web and via Web Services interfaces for users who require systematic access or want to interface with customized pipe-lines and workflows using common programming languages. The framework features novel result visualizations and integration of domain and functional predictions for protein database searches. It is available at http://www.ebi.ac.uk/Tools/sss for sequence similarity searches and at http://www.ebi.ac.uk/Tools/msa for multiple sequence alignments.},
  AUTHOR = {Goujon, Mickael and McWilliam, Hamish and Li, Weizhong and Valentin, Franck and Squizzato, Silvano and Paern, Juri and Lopez, Rodrigo},
  URL = {https://doi.org/10.1093/nar/gkq313},
  DATE = {2010-07},
  DOI = {10.1093/nar/gkq313},
  EPRINT = {https://academic.oup.com/nar/article-pdf/38/suppl_2/W695/3832907/gkq313.pdf},
  ISSN = {0305-1048},
  JOURNALTITLE = {Nucleic Acids Research},
  NUMBER = {2},
  PAGES = {W695--W699},
  TITLE = {A new bioinformatics analysis tools framework at EMBL–EBI},
  VOLUME = {38},
}

@ARTICLE{Madeira2024,
  ABSTRACT = {The EMBL-EBI Job Dispatcher sequence analysis tools framework (https://www.ebi.ac.uk/jdispatcher) enables the scientific community to perform a diverse range of sequence analyses using popular bioinformatics applications. Free access to the tools and required sequence datasets is provided through user-friendly web applications, as well as via RESTful and SOAP-based APIs. These are integrated into popular EMBL-EBI resources such as UniProt, InterPro, ENA and Ensembl Genomes. This paper overviews recent improvements to Job Dispatcher, including its brand new website and documentation, enhanced visualisations, improved job management, and a rising trend of user reliance on the service from low- and middle-income regions.},
  AUTHOR = {Madeira, Fábio and Madhusoodanan, Nandana and Lee, Joonheung and Eusebi, Alberto and Niewielska, Ania and Tivey, Adrian R N and Lopez, Rodrigo and Butcher, Sarah},
  URL = {https://doi.org/10.1093/nar/gkae241},
  DATE = {2024-07},
  DOI = {10.1093/nar/gkae241},
  EPRINT = {https://academic.oup.com/nar/article-pdf/52/W1/W521/58436149/gkae241.pdf},
  ISSN = {0305-1048},
  JOURNALTITLE = {Nucleic Acids Research},
  NUMBER = {W1},
  PAGES = {W521--W525},
  TITLE = {The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024},
  VOLUME = {52},
}