Journal ArticleDOI
Multiple Sequence Alignment Using ClustalW and ClustalX
TLDR
The protocols in this unit discuss how to use ClustalX and ClUSTalW to construct an alignment, and create profile alignments by merging existing alignments.Abstract:
The Clustal programs are widely used for carrying out automatic multiple alignment of nucleotide or amino acid sequences. The most familiar version is ClustalW, which uses a simple text menu system that is portable to more or less all computer systems. ClustalX features a graphical user interface and some powerful graphical utilities for aiding the interpretation of alignments and is the preferred version for interactive usage. Users may run Clustal remotely from several sites using the Web or the programs may be downloaded and run locally on PCs, Macintosh, or Unix computers. The protocols in this unit discuss how to use ClustalX and ClustalW to construct an alignment, and create profile alignments by merging existing alignments.read more
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The Pfam protein families database
Marco Punta,Penny Coggill,Ruth Y. Eberhardt,Jaina Mistry,John Tate,Chris Boursnell,Ningze Pang,Kristoffer Forslund,Goran Ceric,Jody Clements,Andreas Heger,Liisa Holm,Erik L. L. Sonnhammer,Sean R. Eddy,Alex Bateman,Robert D. Finn +15 more
TL;DR: The definition and use of family-specific, manually curated gathering thresholds are explained and some of the features of domains of unknown function (also known as DUFs) are discussed, which constitute a rapidly growing class of families within Pfam.
Journal ArticleDOI
Pfam: the protein families database.
Robert D. Finn,Alex Bateman,Jody Clements,Penelope Coggill,Ruth Y. Eberhardt,Sean R. Eddy,Andreas Heger,Kirstie Hetherington,Liisa Holm,Jaina Mistry,Erik L. L. Sonnhammer,John Tate,Marco Punta +12 more
TL;DR: Pfam as discussed by the authors is a widely used database of protein families, containing 14 831 manually curated entries in the current version, version 27.0, and has been updated several times since 2012.
Journal ArticleDOI
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
Mingxun Wang,Jeremy Carver,Vanessa V. Phelan,Laura M. Sanchez,Neha Garg,Yao Peng,Don D. Nguyen,Jeramie D. Watrous,Clifford A. Kapono,Tal Luzzatto-Knaan,Carla Porto,Amina Bouslimani,Alexey V. Melnik,Michael J. Meehan,Wei-Ting Liu,Max Crüsemann,Paul D. Boudreau,Eduardo Esquenazi,Mario Sandoval-Calderón,Roland D. Kersten,Laura A. Pace,Robert A. Quinn,Katherine R. Duncan,Cheng-Chih Hsu,Dimitrios J. Floros,Ronnie G. Gavilan,Karin Kleigrewe,Trent R. Northen,Rachel J. Dutton,Delphine Parrot,Erin E. Carlson,Bertrand Aigle,Charlotte Frydenlund Michelsen,Lars Jelsbak,Christian Sohlenkamp,Pavel A. Pevzner,Anna Edlund,Anna Edlund,Jeffrey S. McLean,Jeffrey S. McLean,Jörn Piel,Brian T. Murphy,Lena Gerwick,Chih-Chuang Liaw,Yu-Liang Yang,Hans-Ulrich Humpf,Maria Maansson,Robert A. Keyzers,Amy C. Sims,Andrew R. Johnson,Ashley M. Sidebottom,Brian E. Sedio,Andreas Klitgaard,Charles B. Larson,Charles B. Larson,Cristopher A. Boya P.,Daniel Torres-Mendoza,David Gonzalez,Denise Brentan Silva,Denise Brentan Silva,Lucas Miranda Marques,Daniel P. Demarque,Egle Pociute,Ellis C. O’Neill,Enora Briand,Enora Briand,Eric J. N. Helfrich,Eve A. Granatosky,Evgenia Glukhov,Florian Ryffel,Hailey Houson,Hosein Mohimani,Jenan J. Kharbush,Yi Zeng,Julia A. Vorholt,Kenji L. Kurita,Pep Charusanti,Kerry L. McPhail,Kristian Fog Nielsen,Lisa Vuong,Maryam Elfeki,Matthew F. Traxler,Niclas Engene,Nobuhiro Koyama,Oliver B. Vining,Ralph S. Baric,Ricardo Pianta Rodrigues da Silva,Samantha J. Mascuch,Sophie Tomasi,Stefan Jenkins,Venkat R. Macherla,Thomas Hoffman,Vinayak Agarwal,Philip G. Williams,Jingqui Dai,Ram P. Neupane,Joshua R. Gurr,Andrés M. C. Rodríguez,Anne Lamsa,Chen Zhang,Kathleen Dorrestein,Brendan M. Duggan,Jehad Almaliti,Pierre-Marie Allard,Prasad Phapale,Louis-Félix Nothias,Theodore Alexandrov,Marc Litaudon,Jean-Luc Wolfender,Jennifer E. Kyle,Thomas O. Metz,Tyler Peryea,Dac-Trung Nguyen,Danielle VanLeer,Paul Shinn,Ajit Jadhav,Rolf Müller,Katrina M. Waters,Wenyuan Shi,Xueting Liu,Lixin Zhang,Rob Knight,Paul R. Jensen,Bernhard O. Palsson,Kit Pogliano,Roger G. Linington,Marcelino Gutiérrez,Norberto Peporine Lopes,William H. Gerwick,William H. Gerwick,Bradley S. Moore,Bradley S. Moore,Pieter C. Dorrestein,Pieter C. Dorrestein,Nuno Bandeira,Nuno Bandeira +135 more
TL;DR: In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations and data-driven social-networking should facilitate identification of spectra and foster collaborations.
Journal ArticleDOI
Ancestral polyploidy in seed plants and angiosperms
Yuannian Jiao,Norman J. Wickett,Saravanaraj Ayyampalayam,André S. Chanderbali,Lena Landherr,Paula E. Ralph,Lynn P. Tomsho,Yi Hu,Haiying Liang,Pamela S. Soltis,Douglas E. Soltis,Sandra W. Clifton,Scott E. Schlarbaum,Stephan C. Schuster,Hong Ma,Jim Leebens-Mack,Claude W. dePamphilis +16 more
TL;DR: Comprehensive phylogenomic analyses of sequenced plant genomes and more than 12.6 million new expressed-sequence-tag sequences from phylogenetically pivotal lineages are used to elucidate two groups of ancient gene duplications, implicating two WGDs in ancestral lineages shortly before the diversification of extant seed plants and extant angiosperms.
Journal ArticleDOI
Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin
Ryan D. Morin,Nathalie A. Johnson,Tesa M. Severson,Andrew J. Mungall,Jianghong An,Rodrigo Goya,Paul Je,Merrill Boyle,Bruce Woolcock,Florian Kuchenbauer,Damian Yap,Humphries Rk,Obi L. Griffith,Sohrab P. Shah,Hao Zhu,Kimbara M,Shashkin P,Charlot Jf,Tcherpakov M,Richard Corbett,Angela K Y Tam,Richard Varhol,Duane E Smailus,Michelle Moksa,Yongjun Zhao,Allen Delaney,Hong Qian,Inanc Birol,Jacquie Schein,Richard A. Moore,Robert A. Holt,Douglas E. Horsman,Joseph M. Connors,Joseph M. Connors,Steven J.M. Jones,Samuel Aparicio,Martin Hirst,Randy D. Gascoyne,Marco A. Marra,Marco A. Marra +39 more
TL;DR: Recurrent somatic mutations affecting the polycomb-group oncogene EZH2, which encodes a histone methyltransferase responsible for trimethylating Lys27 of histone H3 (H3K27), are reported, consistent with the notion that EZh2 proteins with mutant Tyr641 have reduced enzymatic activity in vitro.
References
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Journal ArticleDOI
Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
TL;DR: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.
Journal ArticleDOI
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Naruya Saitou,Masatoshi Nei +1 more
TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
Journal ArticleDOI
Confidence limits on phylogenies: an approach using the bootstrap.
TL;DR: The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters.
Journal ArticleDOI
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
TL;DR: ClUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W, providing an integrated system for performing multiple sequence and profile alignments and analysing the results.
Journal ArticleDOI
A general method applicable to the search for similarities in the amino acid sequence of two proteins
TL;DR: A computer adaptable method for finding similarities in the amino acid sequences of two proteins has been developed and it is possible to determine whether significant homology exists between the proteins to trace their possible evolutionary development.