Literature DB >> 29035372

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets.

Martin Steinegger1,2, Johannes Söding1.   

Abstract

Mesh:

Year:  2017        PMID: 29035372     DOI: 10.1038/nbt.3988

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN: 1087-0156            Impact factor:   54.908


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  21 in total

Review 1.  From genomics to metagenomics.

Authors:  Narayan Desai; Dion Antonopoulos; Jack A Gilbert; Elizabeth M Glass; Folker Meyer
Journal:  Curr Opin Biotechnol       Date:  2012-01-05       Impact factor: 9.740

Review 2.  Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis.

Authors:  Matthew B Scholz; Chien-Chi Lo; Patrick S G Chain
Journal:  Curr Opin Biotechnol       Date:  2011-12-09       Impact factor: 9.740

3.  Ocean plankton. Structure and function of the global ocean microbiome.

Authors:  Shinichi Sunagawa; Luis Pedro Coelho; Samuel Chaffron; Jens Roat Kultima; Karine Labadie; Guillem Salazar; Bardya Djahanschiri; Georg Zeller; Daniel R Mende; Adriana Alberti; Francisco M Cornejo-Castillo; Paul I Costea; Corinne Cruaud; Francesco d'Ovidio; Stefan Engelen; Isabel Ferrera; Josep M Gasol; Lionel Guidi; Falk Hildebrand; Florian Kokoszka; Cyrille Lepoivre; Gipsi Lima-Mendez; Julie Poulain; Bonnie T Poulos; Marta Royo-Llonch; Hugo Sarmento; Sara Vieira-Silva; Céline Dimier; Marc Picheral; Sarah Searson; Stefanie Kandels-Lewis; Chris Bowler; Colomban de Vargas; Gabriel Gorsky; Nigel Grimsley; Pascal Hingamp; Daniele Iudicone; Olivier Jaillon; Fabrice Not; Hiroyuki Ogata; Stephane Pesant; Sabrina Speich; Lars Stemmann; Matthew B Sullivan; Jean Weissenbach; Patrick Wincker; Eric Karsenti; Jeroen Raes; Silvia G Acinas; Peer Bork
Journal:  Science       Date:  2015-05-22       Impact factor: 47.728

Review 4.  Sequencing and beyond: integrating molecular 'omics' for microbial community profiling.

Authors:  Eric A Franzosa; Tiffany Hsu; Alexandra Sirota-Madi; Afrah Shafquat; Galeb Abu-Ali; Xochitl C Morgan; Curtis Huttenhower
Journal:  Nat Rev Microbiol       Date:  2015-04-27       Impact factor: 60.633

5.  A new repeat-masking method enables specific detection of homologous sequences.

Authors:  Martin C Frith
Journal:  Nucleic Acids Res       Date:  2010-11-24       Impact factor: 16.971

6.  Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation.

Authors:  Torbjørn Rognes
Journal:  BMC Bioinformatics       Date:  2011-06-01       Impact factor: 3.169

7.  The Pacific Ocean virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology.

Authors:  Bonnie L Hurwitz; Matthew B Sullivan
Journal:  PLoS One       Date:  2013-02-28       Impact factor: 3.240

8.  eggNOG: automated construction and annotation of orthologous groups of genes.

Authors:  Lars Juhl Jensen; Philippe Julien; Michael Kuhn; Christian von Mering; Jean Muller; Tobias Doerks; Peer Bork
Journal:  Nucleic Acids Res       Date:  2007-10-16       Impact factor: 16.971

9.  Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.

Authors:  Ebrahim Afshinnekoo; Cem Meydan; Shanin Chowdhury; Dyala Jaroudi; Collin Boyer; Nick Bernstein; Julia M Maritz; Darryl Reeves; Jorge Gandara; Sagar Chhangawala; Sofia Ahsanuddin; Amber Simmons; Timothy Nessel; Bharathi Sundaresh; Elizabeth Pereira; Ellen Jorgensen; Sergios-Orestis Kolokotronis; Nell Kirchberger; Isaac Garcia; David Gandara; Sean Dhanraj; Tanzina Nawrin; Yogesh Saletore; Noah Alexander; Priyanka Vijay; Elizabeth M Hénaff; Paul Zumbo; Michael Walsh; Gregory D O'Mullan; Scott Tighe; Joel T Dudley; Anya Dunaif; Sean Ennis; Eoghan O'Halloran; Tiago R Magalhaes; Braden Boone; Angela L Jones; Theodore R Muth; Katie Schneider Paolantonio; Elizabeth Alter; Eric E Schadt; Jeanne Garbarino; Robert J Prill; Jane M Carlton; Shawn Levy; Christopher E Mason
Journal:  Cell Syst       Date:  2015-03-03       Impact factor: 10.304

10.  The Pfam protein families database: towards a more sustainable future.

Authors:  Robert D Finn; Penelope Coggill; Ruth Y Eberhardt; Sean R Eddy; Jaina Mistry; Alex L Mitchell; Simon C Potter; Marco Punta; Matloob Qureshi; Amaia Sangrador-Vegas; Gustavo A Salazar; John Tate; Alex Bateman
Journal:  Nucleic Acids Res       Date:  2015-12-15       Impact factor: 16.971

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  336 in total

1.  Accurate Annotation of Microbial Metagenomic Genes and Identification of Core Sets.

Authors:  Chiara Vanni
Journal:  Methods Mol Biol       Date:  2021

2.  CRISPR Arrays Away from cas Genes.

Authors:  Sergey A Shmakov; Irina Utkina; Yuri I Wolf; Kira S Makarova; Konstantin V Severinov; Eugene V Koonin
Journal:  CRISPR J       Date:  2020-12

3.  Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species.

Authors:  Arnaud Belcour; Clémence Frioux; Méziane Aite; Anthony Bretaudeau; Falk Hildebrand; Anne Siegel
Journal:  Elife       Date:  2020-12-29       Impact factor: 8.140

4.  Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution.

Authors:  Jingqiu Liao; Xiaodong Guo; Daniel L Weller; Shaul Pollak; Daniel H Buckley; Martin Wiedmann; Otto X Cordero
Journal:  Nat Microbiol       Date:  2021-07-15       Impact factor: 17.745

5.  Seeker: alignment-free identification of bacteriophage genomes by deep learning.

Authors:  Noam Auslander; Ayal B Gussow; Sean Benler; Yuri I Wolf; Eugene V Koonin
Journal:  Nucleic Acids Res       Date:  2020-12-02       Impact factor: 16.971

Review 6.  Benchmarking Metagenomics Tools for Taxonomic Classification.

Authors:  Simon H Ye; Katherine J Siddle; Daniel J Park; Pardis C Sabeti
Journal:  Cell       Date:  2019-08-08       Impact factor: 41.582

7.  Prokaryotic viperins produce diverse antiviral molecules.

Authors:  Aude Bernheim; Adi Millman; Gal Ofir; Gilad Meitav; Carmel Avraham; Helena Shomar; Masha M Rosenberg; Nir Tal; Sarah Melamed; Gil Amitai; Rotem Sorek
Journal:  Nature       Date:  2020-09-16       Impact factor: 49.962

8.  Identification of a distinct lineage of aviadenovirus from crane feces.

Authors:  Yahiro Mukai; Yuriko Tomita; Kirill Kryukov; So Nakagawa; Makoto Ozawa; Tsutomu Matsui; Keizo Tomonaga; Tadashi Imanishi; Yoshihiro Kawaoka; Tokiko Watanabe; Masayuki Horie
Journal:  Virus Genes       Date:  2019-09-23       Impact factor: 2.332

9.  Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems.

Authors:  Adi Millman; Sarah Melamed; Gil Amitai; Rotem Sorek
Journal:  Nat Microbiol       Date:  2020-08-24       Impact factor: 17.745

10.  Diverse enzymatic activities mediate antiviral immunity in prokaryotes.

Authors:  Linyi Gao; Han Altae-Tran; Francisca Böhning; Kira S Makarova; Michael Segel; Jonathan L Schmid-Burgk; Jeremy Koob; Yuri I Wolf; Eugene V Koonin; Feng Zhang
Journal:  Science       Date:  2020-08-28       Impact factor: 47.728

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