Multiple sequence alignment with the Clustal series of programs
Ramu Chenna,Hideaki Sugawara,Tadashi Koike,Rodrigo Lopez,Toby J. Gibson,Desmond G. Higgins,Julie D. Thompson +6 more
TLDR
The Clustal series of programs, widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees, are extended.Abstract:
The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also the robustness, portability and user-friendliness of the programs. New features include NEXUS and FASTA format output, printing range numbers and faster tree calculation. Although, Clustal was originally developed to run on a local computer, numerous Web servers have been set up, notably at the EBI (European Bioinformatics Institute) (http://www.ebi.read more
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UCSF Chimera--a visualization system for exploratory research and analysis.
Eric F. Pettersen,Thomas D. Goddard,Conrad C. Huang,Gregory S. Couch,Daniel M. Greenblatt,Elaine C. Meng,Thomas E. Ferrin +6 more
TL;DR: Two unusual extensions are presented: Multiscale, which adds the ability to visualize large‐scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales.
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RDP3: a flexible and fast computer program for analyzing recombination
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SELEX--a (r)evolutionary method to generate high-affinity nucleic acid ligands.
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Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite.
Falk Warnecke,Peter Luginbuhl,Natalia Ivanova,Majid Ghassemian,Toby Richardson,Toby Richardson,Justin T. Stege,Michelle H. Cayouette,Alice C. McHardy,Gordana Djordjevic,Nahla Aboushadi,Rotem Sorek,Susannah G. Tringe,Mircea Podar,Hector Garcia Martin,Victor Kunin,Daniel Dalevi,Julita Madejska,Edward Kirton,Darren Platt,Ernest Szeto,Asaf Salamov,Kerrie Barry,Natalia Mikhailova,Nikos C. Kyrpides,Eric G. Matson,Elizabeth A. Ottesen,Xinning Zhang,Myriam Hernandez,Catalina Patricia Morales Murillo,Luis G. Acosta,Isidore Rigoutsos,Giselle Tamayo,Brian D. Green,Cathy Chang,Edward M. Rubin,Eric J. Mathur,Eric J. Mathur,Dan E. Robertson,Philip Hugenholtz,Jared R. Leadbetter +40 more
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Critical Evaluation of Two Primers Commonly Used for Amplification of Bacterial 16S rRNA Genes
Jeremy A. Frank,Claudia I. Reich,Shobha Sharma,Jon S. Weisbaum,Jon S. Weisbaum,Brenda A. Wilson,Gary J. Olsen +6 more
TL;DR: This work proposes a formulation for a forward primer (27f) that includes three sequences not usually present that is better at maintaining the original rRNA gene ratio of Lactobacillus spp.
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
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
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
CLUSTAL: A package for performing multiple sequence alignment on a microcomputer
Desmond G. Higgins,Paul M. Sharp +1 more
TL;DR: An approach for performing multiple alignments of large numbers of amino acid or nucleotide sequences is described, based on first deriving a phylogenetic tree from a matrix of all pairwise sequence similarity scores obtained using a fast pairwise alignment algorithm.
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