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HMMER web server: 2018 update

Simon C Potter, Aurélien Luciani, Sean R Eddy, Youngmi Park, Rodrigo Lopez, Robert D Finn
2018 Nucleic Acids Research  
the HMMER software suite (http://hmmer.org).  ...  The HMMER webserver [http://www.ebi.ac.uk/Tools/ hmmer] is a free-to-use service which provides fast searches against widely used sequence databases and profile hidden Markov model (HMM) libraries using  ...  web server.  ... 
doi:10.1093/nar/gky448 pmid:29905871 pmcid:PMC6030962 fatcat:k3vsfblq5ba3tkdhcp57ufiq5q

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

Han Zhang, Tanner Yohe, Le Huang, Sarah Entwistle, Peizhi Wu, Zhenglu Yang, Peter K Busk, Ying Xu, Yanbin Yin
2018 Nucleic Acids Research  
Here, dbCAN2 (http://cys.bios. niu.edu/dbCAN2) is presented as an updated meta server, which integrates three state-of-the-art tools for CAZome (all CAZymes of a genome) annotation: (i) HMMER search against  ...  We developed the dbCAN web server in 2012 to provide a public service for automated CAZyme annotation for newly sequenced genomes.  ...  W100 Nucleic Acids Research, 2018, Vol. 46, Web Server issue Nucleic Acids Research, 2018, Vol. 46, Web Server issue W97 • HMMER vs. dbCAN • DIAMOND vs. CAZy • Hotpep vs.  ... 
doi:10.1093/nar/gky418 pmid:29771380 pmcid:PMC6031026 fatcat:b6hakpsrgbhvlotq5gdfddznjq

Editorial: The 16th annual Nucleic Acids Research web server issue 2018

2018 Nucleic Acids Research  
Table 1 lists the 2018 web servers, their URLs, and a brief description of each. Topics.  ...  The 2018 web server issue of Nucleic Acids Research is the 16th in a series of annual issues dedicated to web-based software resources for analysis and visualization of molecular biology data.  ...  Acknowledgements: The web server issue arises out of the work of many people who I would like to thank.  ... 
doi:10.1093/nar/gky518 pmid:29982807 pmcid:PMC6030837 fatcat:x7lzti7w2nhp5elvqmg5at77rq

AbPredict 2: a server for accurate and unstrained structure prediction of antibody variable domains

2018 Bioinformatics  
We present the AbPredict 2 web-server, which instead of using sequence homology, conducts a Monte Carlo-based search for low-energy combinations of backbone conformations to yield accurate and unstrained  ...  Scripts, documentation, and instructions for executing AbPredict 2 independent of the web server are available in http://www.rosettacommons.org.  ...  Implementation With the intent of developing a fully automated web-server for non-expert users, AbPredict 2 only requires a fasta-formatted sequence of the query antibody.  ... 
doi:10.1093/bioinformatics/bty822 pmid:30951584 pmcid:PMC6542689 fatcat:fqtkv4lmtngc5njccmzpqbvvqy

LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins

2019 Nucleic Acids Research  
threading approaches, (ii) deep sequence search-based sequence profile construction and (iii) a new web interface design that incorporates structure-based function annotations.  ...  The LOMETS2 server (https://zhanglab.ccmb.med.umich.edu/LOMETS/) is an online meta-threading server system for template-based protein structure prediction.  ...  WEB SERVER Server input The input to the LOMETS2 server is a single-chain amino acid sequence file in FASTA format.  ... 
doi:10.1093/nar/gkz384 pmid:31081035 pmcid:PMC6602514 fatcat:4xzeqfsqgncwrlxepe3stwo3ou

WaspBase: a genomic resource for the interactions among parasitic wasps, insect hosts and plants

Longfei Chen, Kun Lang, Shoudong Bi, Jiapeng Luo, Feiling Liu, Xinhai Ye, Jiadan Xu, Kang He, Fei Li, Gongyin Ye, Xuexin Chen
2018 Database: The Journal of Biological Databases and Curation  
WaspBase provides conventional web services such as Basic Local Alignment Search Tool, search and download, together with several widely used tools such as profile hidden Markov model, Multiple Alignment  ...  A web server of HMMER is provided to search sequence homologs and to make sequence alignments. It uses probabilistic models called profile hidden Markov models (profile HMMs) (39) .  ...  The Apache server handles queries from web clients through PHP scripts to perform searches.  ... 
doi:10.1093/database/bay081 pmid:30219838 pmcid:PMC6146128 fatcat:xikkukz2q5c6riaed32fzfhsli

PHAST: A Fast Phage Search Tool

Y. Zhou, Y. Liang, K. H. Lynch, J. J. Dennis, D. S. Wishart
2011 Nucleic Acids Research  
PHAge Search Tool (PHAST) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids.  ...  K.H.L. co-designed the methods and tested the server. D.S.W. and J.J.D. conceived the ideas, server requirements and general methodology.  ...  Y.L. prepared the phage and bacterial sequence databases, built the web interface and implemented various external programs (BLAST, GLIMMER, CGVIEW).  ... 
doi:10.1093/nar/gkr485 pmid:21672955 pmcid:PMC3125810 fatcat:bfz7lyio3fbz7germhaf6qwl24

Wei2GO: weighted sequence similarity-based protein function prediction [article]

Maarten JMF Reijnders
2020 bioRxiv   pre-print
Such local versions are necessary to perform large scale genomics studies due to the absence of any limitations imposed by web servers such as queues, prediction speed, and updatability of reference data  ...  It is compared against the Argot2 and Argot2.5 web servers, which use a similar concept.  ...  Results Wei2GO is made to facilitate open-source protein function prediction, and the ability to do this independent of web-servers. Two of these web-servers, Argot2.5 and its predecessor .  ... 
doi:10.1101/2020.04.24.059501 fatcat:h3dnu2me5zfcdkkidpsksumymy

A TALE of shrimps: Genome-wide survey of homeobox genes in 120 species from diverse crustacean taxa

Wai Hoong Chang, Alvina G. Lai
2018 F1000Research  
PubMed Abstract | Publisher Full Text | Free Full Text Finn RD, Clements J, Arndt W, et al.: HMMER web server: 2015 update. Nucleic Acids Res. 2015; 43(W1): W30-W38.  ...  PubMed Abstract | Publisher Full Text | Free Full Text Finn RD, Clements J, Eddy SR: HMMER web server: interactive sequence similarity searching.  ...  DOI, 10.5256/f1000research.13636.d190418 (Chang & Lai, 2018). genes: new conserved motifs and cases of accelerated evolution. J Mol Evol. F1000Research 2018, 7:71 Last updated: 17 JAN 2018  ... 
doi:10.12688/f1000research.13636.1 pmid:29899973 pmcid:PMC5968366 fatcat:dm6l7h26u5d6bhy7du7v3eia5u

oriTfinder: a web-based tool for the identification of origin of transfers in DNA sequences of bacterial mobile genetic elements

Xiaobin Li, Yingzhou Xie, Meng Liu, Cui Tai, Jingyong Sun, Zixin Deng, Hong-Yu Ou
2018 Nucleic Acids Research  
oriTfinder is a web server that facilitates the rapid identification of the origin of transfer site (oriT) of a conjugative plasmid or chromosome-borne integrative and conjugative element.  ...  The server also detects the other transfer-related modules, including the potential relaxase gene, T4CP gene and the type IV secretion system gene cluster, and the putative genes coding for virulence factors  ...  46, Web Server issue W231 Figure 1 .  ... 
doi:10.1093/nar/gky352 pmid:29733379 pmcid:PMC6030822 fatcat:oxqkjfrbfrew5avm2pina6jlba

AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors

Hui Hu, Ya-Ru Miao, Long-Hao Jia, Qing-Yang Yu, Qiong Zhang, An-Yuan Guo
2018 Nucleic Acids Research  
The AnimalTFDB has been maintained and updated for seven years and we will continue to improve it.  ...  Recently, we updated the AnimalTFDB to version 3.0 (http://bioinfo.life.hust.edu.cn/AnimalTFDB/) with more data and functions to improve it.  ...  It also retains the web servers 'Predict TF', 'Predict TFBS' and 'Blast' tool.  ... 
doi:10.1093/nar/gky822 pmid:30204897 fatcat:f6xyu6w46jb7lgog5do72e3mzy

The Ocean Gene Atlas: exploring the biogeography of plankton genes online

Emilie Villar, Thomas Vannier, Caroline Vernette, Magali Lescot, Miguelangel Cuenca, Aurélien Alexandre, Paul Bachelerie, Thomas Rosnet, Eric Pelletier, Shinichi Sunagawa, Pascal Hingamp
2018 Nucleic Acids Research  
The Ocean Gene Atlas is a web service to explore the biogeography of genes from marine planktonic organisms.  ...  Ocean Gene Atlas is a freely-available web service at: http://tara-oceans.mio.osupytheas.fr/oceangene-atlas/.  ...  The PHP application server queries abun-Nucleic Acids Research, 2018, Vol. 46, Web Server issue W293 dance and environmental data stored in a MySQL relational database.  ... 
doi:10.1093/nar/gky376 pmid:29788376 pmcid:PMC6030836 fatcat:raoyacej7ja2fkfzbcafnry2ya

Profile Comparer Extended: phylogeny of lytic polysaccharide monooxygenase families using profile hidden Markov model alignments

Gerben P. Voshol, Peter J. Punt, Erik Vijgenboom
2019 F1000Research  
After generating the initial dataset, the taxonomic distribution and the presence of accessory domains were analyzed using the HMMER web server (Potter et al., 2018) .  ...  Taxonomic occurrence and domain organization After the initial dataset was created, the taxonomic occurrence and domain organization were analyzed using the HMMER web server (Potter et al., 2018) .  ...  It is plausible that the authors updated the popular original PRC program with the ability to load HMMer3.0 pHMM files, this is a very desired feature among the users of the original PRC program.  ... 
doi:10.12688/f1000research.21104.1 pmid:31956399 pmcid:PMC6950343 fatcat:224uohbx45g7zm6rkydsfo6usy

Pise: Software for building bioinformatics webs

D. Gilbert
2002 Briefings in Bioinformatics  
It creates common, easy-to-use interfaces to these applications for the Web, or other uses.  ...  It is adaptable to new bioinformatics tools, and offers program chaining, Unix system batch and other controls, making it an attractive method for building and using your own bioinformatics web services  ...  server on your computer.  ... 
doi:10.1093/bib/3.4.405 pmid:12511068 fatcat:dw77hayqnzcobig656h7glgjbe

The SUPERFAMILY database in 2004: additions and improvements

M. Madera
2004 Nucleic Acids Research  
The complete results including alignments are available from the webserver as either individual web pages for online browsing,¯at ®les or MySQL dumps for bulk download, or via a Distrubed Annotation Server  ...  Distributed annotation server (DAS) All SUPERFAMILY genome assignments are available via a protein DAS server (see http://biodas.org for more information).  ... 
doi:10.1093/nar/gkh117 pmid:14681402 pmcid:PMC308851 fatcat:ja7yohpxorgrbdq7nhm4xcf4qq
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