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HMMER web server: 2018 update
2018
Nucleic Acids Research
Preserved Fulltext
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
2018
Nucleic Acids Research
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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
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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
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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
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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
2018
Database: The Journal of Biological Databases and Curation
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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
2011
Nucleic Acids Research
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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]
2020
bioRxiv
pre-print
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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
2018
F1000Research
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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
2018
Nucleic Acids Research
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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
2018
Nucleic Acids Research
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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
2018
Nucleic Acids Research
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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
2019
F1000Research
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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
2002
Briefings in Bioinformatics
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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
2004
Nucleic Acids Research
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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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