Filters








1,913 Hits in 3.3 sec

The TIGRFAMs database of protein families

D. H. Haft
<span title="2003-01-01">2003</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The database currently contains over 1600 protein families. TIGRFAMs is available for searching or downloading at www.tigr.org/TIGRFAMs.  ...  TIGRFAMs is a collection of manually curated protein families consisting of hidden Markov models (HMMs), multiple sequence alignments, commentary, Gene Ontology (GO) assignments, literature references  ...  The salient feature of TIGRFAMs is the tuning of the breadth of each protein family to serve the needs of genome annotation.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkg128">doi:10.1093/nar/gkg128</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12520025">pmid:12520025</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC165575/">pmcid:PMC165575</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ljk4hkntfff7tnufkmyp7erd5q">fatcat:ljk4hkntfff7tnufkmyp7erd5q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190219072222/http://pdfs.semanticscholar.org/1789/1bdbfec1950f7c361db96dca043cfbf54769.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/17/89/17891bdbfec1950f7c361db96dca043cfbf54769.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkg128"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC165575" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

TIGRFAMs and Genome Properties in 2013

Daniel H. Haft, Jeremy D. Selengut, Roland A. Richter, Derek Harkins, Malay K. Basu, Erin Beck
<span title="2012-11-28">2012</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
TIGRFAMs, available online at http://www.jcvi.org/ tigrfams is a database of protein family definitions.  ...  Each TIGRFAM as a proxy for a curatorial expert in that protein family The TIGRFAMs database provides manually reviewed definitions of protein families with the following characteristics to make them useful  ...  The process of systems reconstruction in Genome Properties provides guidance for protein family construction in TIGRFAMs, so the two databases develop in concert.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gks1234">doi:10.1093/nar/gks1234</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23197656">pmid:23197656</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3531188/">pmcid:PMC3531188</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ky727p5f6zasfhv7xwzustjw6i">fatcat:ky727p5f6zasfhv7xwzustjw6i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170715124231/https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/nar/41/D1/10.1093/nar/gks1234/2/gks1234.pdf?Expires=1500216151&amp;Signature=SMOr3T8TwAc0qzdg79MYcpo79evMcdoqGv2DXHiOkObEFUTDt9JUOaOaumFaxvbJdjrsl11gAgAgsCTcWCxGXf9r4NcGRUzr9xKPkgg5jFfbOOMKK6Ix9YnTdcATY-Xspojii3~9bVuLjJnQmDd9Y09y8Dv9R47RbB2tV-Q68f2WSLXFBX-ujIxiqIyFqECi2gtFOZthECTpNaULQ~vfELmdDiNPL8u2gxKDbo9V-pAXJ1OrWRGAdF6M9vaeATYBkCaxIfg6OozKnpas6C1Bpf9n6v-iHs6omzNFuMNTCvnh50L0zmIF-JwW0RJmTBFimmkg-mUiG2gWEbY2evn-dA__&amp;Key-Pair-Id=APKAIUCZBIA4LVPAVW3Q" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ef/b0/efb0dc7331d08c3778bae00a56755d22df8f4ca1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gks1234"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531188" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

HMM-based databases in InterPro

A. Bateman
<span title="2002-01-01">2002</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
This paper reviews the Pfam, TIGRFAMs and SMART databases that use the profile-HMMs provided by the HMMER package.  ...  Protein family databases are an important resource for protein annotation and understanding protein evolution and function.  ...  INTRODUCTION Protein family databases have become a key tool in the armoury of the molecular biologist as well as the dedicated computational biologist.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/3.3.236">doi:10.1093/bib/3.3.236</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12230032">pmid:12230032</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ykxhgzgngrbblmc3zbwdrpsf7q">fatcat:ykxhgzgngrbblmc3zbwdrpsf7q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170716191305/https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bib/3/3/10.1093/bib/3.3.236/2/236.pdf?Expires=1500325985&amp;Signature=QeKJPBzvn~KkOWj5Rqmc-rY8J4i0zYfwgbloFAFYZl1D6QWMNmwmeVeu2-Kx8GZGgvOaKBPGVJowOKxcjyeMUj2N3RFbj1OL7IOIfNF5-ZhoZy-fQ-O0Hsa3T~ZoZnvl~fIxDN7UxiPXEgJukYCQ95u7MNAhedEf6gtjsJ7ungMzYD8lrBYBOg8vmLKDpe8-zSIEFWHgd1S750tA~SmnrusN1KmmZxTLs3iaNcdfT8s1UrK-AA57HTlI~KUPTuLzU5Ky-BMBqTV8gKtRrliZRZQ~ncxIG8VMLrV44wbM72iw5rNj5GoIymqxCxwJza~AXfRxe6ASlkAT0w7RpU8-BA__&amp;Key-Pair-Id=APKAIUCZBIA4LVPAVW3Q" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f6/fc/f6fca06252ab2c8e8e2e949b5662945f37ba4eb5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/3.3.236"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes

J. D. Selengut, D. H. Haft, T. Davidsen, A. Ganapathy, M. Gwinn-Giglio, W. C. Nelson, A. R. Richter, O. White
<span title="2007-01-03">2007</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
ACKNOWLEDGEMENTS This work has been supported by grants from the United States National Science Foundation (DBI-0445826), the United States Department of Energy (DE-FG02-04ER63935) and the United States  ...  National Institute of Allergy and Infectious Disease (NIH-NIAID-DMID-04-34, HHSN266200400038C).  ...  The TIGRFAMs database includes 600 models of the 'subfamily' type, many of which represent important divisions among broader protein families from Pfam.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkl1043">doi:10.1093/nar/gkl1043</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17151080">pmid:17151080</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1781115/">pmcid:PMC1781115</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/aert4ty3grffblenyc65cokjfq">fatcat:aert4ty3grffblenyc65cokjfq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180726214848/https://watermark.silverchair.com/gkl1043.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAawwggGoBgkqhkiG9w0BBwagggGZMIIBlQIBADCCAY4GCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMqZA0mkSvjHcbiRO-AgEQgIIBX6kR_W1aeEnqvPCBMhg9zqR3ZMs0Sp4sTWxl1hnziX3KyD6AcX3xDEQX_f2QcUCdlAyh5TgmJBypdLxqTVIfSbFokSkRKBg9uNDiudjFCezuSkhghvvQUwK8U8OkDqYgUd0mwEQfFad2_PVSgzAbgj0GhTf70Dc30DcNOLSnonqCnBbXSnRTZF0_0gOQga5hScuWrnN7rgxf0jemao11iWGDw5DN_27WCywRMwSwY4a8B3siPZaPiwcIEf1cmP5Ic9loJjKCLZDEYOy3QkwEa5kJWvt4f8nLu1cepdKWq4kPuEso_QumZufFVEmMZPOF1GTbDj-qThfY1uVF8diaPYlA7lU0Shu18Rci6wz2Oi2nxnfSKgMc-cm_Ob9rkf-njPxjelm8KkQp9I14SJCLJLzbgEz8RszEVCIUwQLXyxCSr-gxIPajiQUpx6osqPPZfTU9UELCe1-W25zWE_2lIA" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e1/8b/e18b660f4d8092f9ab13735fa1b477bc8ce11de7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkl1043"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1781115" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

TIGRFAMs: a protein family resource for the functional identification of proteins

D. H. Haft
<span title="2001-01-01">2001</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
TIGRFAMs is a collection of protein families featuring curated multiple sequence alignments, hidden Markov models and associated information designed to support the automated functional identification  ...  TIGRFAMs currently contains over 800 protein families, available for searching or downloading at www.tigr.org/TIGRFAMs.  ...  BUILDING TIGRFAMs We have built a collection of protein families, TIGRFAMs, most of which are predicted to have uniform function.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/29.1.41">doi:10.1093/nar/29.1.41</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11125044">pmid:11125044</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC29844/">pmcid:PMC29844</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lvg7x3ypkja7llokui4sqtdjqi">fatcat:lvg7x3ypkja7llokui4sqtdjqi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808185835/https://phylogenomics.files.wordpress.com/2012/02/34-haft-2001-tigrfams.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/74/ee/74ee39c8bb789b3e89e47f87cb1e7b33bb4184bb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/29.1.41"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC29844" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes

Konstantinos Mavromatis, Natalia N. Ivanova, I-Min A. Chen, Ernest Szeto, Victor M. Markowitz, Nikos C. Kyrpides
<span title="2009-07-20">2009</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5xcscx7glffihaolts5vo2ioaa" style="color: black;">Standards in Genomic Sciences</a> </i> &nbsp;
DOE-JGI MAP annotation includes prediction of protein coding and RNA genes, as well as repeats and assignment of product names to these genes.  ...  DOE-JGI MAP annotation is applied on nucleotide sequence datasets included in the IMG-ER (Expert Review) version of IMG via the IMG ER submission site.  ...  Acknowledgments The work presented in this article was performed under the auspices of the US Department of Energy  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4056/sigs.632">doi:10.4056/sigs.632</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21304638">pmid:21304638</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3035208/">pmcid:PMC3035208</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ewknmnkkpvenzjxqj6k7x74biq">fatcat:ewknmnkkpvenzjxqj6k7x74biq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190416064153/https://core.ac.uk/download/pdf/81624061.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f9/7d/f97de3b4ff0d8b59bfab5f66832d83fadf5fe15d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4056/sigs.632"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035208" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

TheViral MetaGenome Annotation Pipeline (VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data

Hernan A. Lorenzi, Jeff Hoover, Jason Inman, Todd Safford, Sean Murphy, Leonid Kagan, Shannon J. Williamson
<span title="2011-06-30">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5xcscx7glffihaolts5vo2ioaa" style="color: black;">Standards in Genomic Sciences</a> </i> &nbsp;
The large volume of sequence data from novel organisms generated by metagenomic projects has triggered the development of specialized databases and tools focused on particular groups of organisms or data  ...  The Viral MetaGenome Annotation Pipeline (VMGAP) pipeline takes advantage of a number of specialized databases, such as collections of mobile genetic elements and environmental metagenomes to improve the  ...  Acknowledgements This research was supported by the Office of Science (BER), U.S. Department of Energy, Cooperative Agreement No.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4056/sigs.1694706">doi:10.4056/sigs.1694706</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21886867">pmid:21886867</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3156399/">pmcid:PMC3156399</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2kb4djzxi5h73im5xsbf7lygny">fatcat:2kb4djzxi5h73im5xsbf7lygny</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171009101118/http://publisher-connector.core.ac.uk/resourcesync/data/Springer-OA/pdf/179/aHR0cDovL2xpbmsuc3ByaW5nZXIuY29tLzEwLjQwNTYvc2lncy4xNjk0NzA2LnBkZg%3D%3D.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/51/c1/51c131337353d575260a89cbda078c9cf3b442aa.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4056/sigs.1694706"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3156399" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score

Hirokazu Chiba, Ikuo Uchiyama
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Moreover, the refined classification showed better agreement than the classifications in the eggNOG databases when TIGRFAMs was used as the reference database.  ...  clusters and TIGRFAMs models as the reference data.  ...  This work was supported by the National Bioscience Database Center, Japan Science Technology Agency.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-15-148">doi:10.1186/1471-2105-15-148</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24885064">pmid:24885064</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4035852/">pmcid:PMC4035852</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pe3vr23265bcpcvusze3luqfzq">fatcat:pe3vr23265bcpcvusze3luqfzq</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC4035852/PMC4035852-1471-2105-15-148.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> File Archive [PDF] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-15-148"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035852" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Significant speedup of database searches with HMMs by search space reduction with PSSM family models

Michael Beckstette, Robert Homann, Robert Giegerich, Stefan Kurtz
<span title="2009-10-14">2009</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
We employ simpler models of protein families called position-specific scoring matrices family models (PSSM-FMs).  ...  Motivation: Profile hidden Markov models (pHMMs) are currently the most popular modeling concept for protein families.  ...  ACKNOWLEDGEMENTS The authors thank Andrew Torda and four anonymous reviewers for comments on the manuscript. Conflict of Interest: none declared.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btp593">doi:10.1093/bioinformatics/btp593</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19828575">pmid:19828575</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2788931/">pmcid:PMC2788931</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ezmxd7rorzgk5boa23ofjlpzba">fatcat:ezmxd7rorzgk5boa23ofjlpzba</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190309183335/http://pdfs.semanticscholar.org/fde8/2f450042267a1a78d0eaaa79883a5d829bd2.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fd/e8/fde82f450042267a1a78d0eaaa79883a5d829bd2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btp593"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788931" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

Marcel Huntemann, Natalia N. Ivanova, Konstantinos Mavromatis, H. James Tripp, David Paez-Espino, Krishnaveni Palaniappan, Ernest Szeto, Manoj Pillay, I-Min A. Chen, Amrita Pati, Torben Nielsen, Victor M. Markowitz (+1 others)
<span title="2015-10-26">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5xcscx7glffihaolts5vo2ioaa" style="color: black;">Standards in Genomic Sciences</a> </i> &nbsp;
The MGAP sequence data processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements.  ...  Structural annotation is followed by assignment of protein product names and functions.  ...  Protein families 1.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s40793-015-0077-y">doi:10.1186/s40793-015-0077-y</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26512311">pmid:26512311</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4623924/">pmcid:PMC4623924</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7dsnixegxjfhhpmxf4xqiwy7ki">fatcat:7dsnixegxjfhhpmxf4xqiwy7ki</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830064447/https://standardsingenomics.biomedcentral.com/track/pdf/10.1186/s40793-015-0077-y?site=http://standardsingenomics.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c2/0e/c20e06881d10b7e243710d5205e148a41bfdaa29.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s40793-015-0077-y"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4623924" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Domains, motifs and clusters in the protein universe

Jinfeng Liu, Burkhard Rost
<span title="">2003</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/o5uh5dlljbbfjm7vgxk2jibrwu" style="color: black;">Current Opinion in Chemical Biology</a> </i> &nbsp;
JL and BR were supported by the grants 1-P50-GM62413-01 and RO1-GM63029-01 from the National Institute of Health (NIH).  ...  Last, not least, thanks to all those who deposit their experimental data in public databases, and to those who maintain these databases.  ...  Expert-curated family databases like Pfam [6•], TIGRFAMs [9] , SMART [7] , and COGs [2] have steadily increased their coverage of the protein universe over the last year.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s1367-5931(02)00003-0">doi:10.1016/s1367-5931(02)00003-0</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12547420">pmid:12547420</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3etuaqalbnbr5hxzdbajd3cdrq">fatcat:3etuaqalbnbr5hxzdbajd3cdrq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20050302015847/http://people.ucsc.edu:80/~anvu/220_Project/2003_rev_cluster.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fb/8f/fb8f41dced7098f019936f9b4f8ebe9892b9c86b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s1367-5931(02)00003-0"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Domains and motifs--proteins in bite-sized chunks

L. Mullan
<span title="2004-01-01">2004</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
The Interpro database is a collection of all the above databases together with SMART 12 which records protein domains involved in cell signalling, TIGRfams 13 -families of domains curated from hidden Markov  ...  Using the system of fingerprints, families of proteins containing these motifs can be established. This is also true of families of proteins containing specific domains.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/5.1.71">doi:10.1093/bib/5.1.71</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15153307">pmid:15153307</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lwlmebnopvf3pc265lr3h7iasi">fatcat:lwlmebnopvf3pc265lr3h7iasi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190308083346/http://pdfs.semanticscholar.org/ef9f/6bbb7bc6b832d84e9411b0e052a142165b58.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ef/9f/ef9f6bbb7bc6b832d84e9411b0e052a142165b58.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/5.1.71"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics

D. H. Haft, J. D. Selengut, L. M. Brinkac, N. Zafar, O. White
<span title="2004-09-03">2004</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
The results of searches using hidden Markov models allow many properties to be deduced automatically, especially for families of proteins (equivalogs) conserved in function since their last common ancestor  ...  Motivation: The presence or absence of metabolic pathways and structures provide a context that makes protein annotation far more reliable.  ...  ACKNOWLEDGEMENTS We would like to thank Tanja Davidsen for her support in integrating Genome Properties into the Comprehensive Microbial Resource.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bti015">doi:10.1093/bioinformatics/bti015</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15347579">pmid:15347579</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hvu237jibrfqfdpzfnrdbqtlf4">fatcat:hvu237jibrfqfdpzfnrdbqtlf4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190221025824/http://pdfs.semanticscholar.org/2d98/370c6b4821a410743c0e8a73f50bc4aa4d8d.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2d/98/2d98370c6b4821a410743c0e8a73f50bc4aa4d8d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bti015"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

The Comprehensive Microbial Resource

J. D. Peterson
<span title="2001-01-01">2001</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The Comprehensive Microbial Resource (CMR) contains robust annotation of all complete microbial genomes and allows for a wide variety of data retrievals.  ...  One challenge presented by large-scale genome sequencing efforts is effective display of uniform information to the scientific community.  ...  The omniome also contains 2104 COGs (1), 996 TIGRFAMs (2) and the results of pre-run searches of all proteins searched against each other.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/29.1.123">doi:10.1093/nar/29.1.123</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11125067">pmid:11125067</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC29848/">pmcid:PMC29848</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nnm2poxehzaztgnexvlz4stsjq">fatcat:nnm2poxehzaztgnexvlz4stsjq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20161209175231/http://andrew-michaelson.com/Genetics/AdditionalPaperstoRead/Regulation_Reading/Jan_10_15/1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/17/59/1759cee556de3f7253515d0e1c9e2fbdb64a4a39.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/29.1.123"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC29848" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

InterPro: An integrated documentation resource for protein families, domains and functional sites

<span title="2002-01-01">2002</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
In recognition of this, InterPro was developed as an integrated documentation resource for protein families, domains and functional sites, to rationalise the complementary efforts of the individual protein  ...  of the resulting protein sequences.  ...  Acknowledgements The InterPro project is supported by the ProFuSe grant (number QLG2-CT-2000-00517) of the European Commission.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/3.3.225">doi:10.1093/bib/3.3.225</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12230031">pmid:12230031</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2igbmarmcjbpfphuwf6l7ny4cy">fatcat:2igbmarmcjbpfphuwf6l7ny4cy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20151004143258/http://www.letunic.com/publications/12230031.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b6/3a/b63a39f7994e276e872b82edf8ba58a5356577bd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/3.3.225"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>
&laquo; Previous Showing results 1 &mdash; 15 out of 1,913 results