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The UCSC Archaeal Genome Browser

K. L. Schneider
2006 Nucleic Acids Research  
We have created a UCSC Archaeal Genome Browser, available at http://archaea.ucsc.edu/, currently with 26 archaeal genomes.  ...  The feature-rich UCSC Genome Browser, created originally to annotate the human genome, can be applied to any sequenced organism.  ...  ACKNOWLEDGEMENTS We thank Jim Kent and the Genome Bioinformatics Group of UC Santa Cruz, in particular Hiram Clawson, for providing the UCSC Genome Browser and assisting us in developing the Archaeal Genome  ... 
doi:10.1093/nar/gkj134 pmid:16381898 pmcid:PMC1347496 fatcat:p3p5d4jb5jfenhbokwzygyo7jm

The UCSC Archaeal Genome Browser: 2012 update

P. P. Chan, A. D. Holmes, A. M. Smith, D. Tran, T. M. Lowe
2011 Nucleic Acids Research  
The UCSC Archaeal Genome Browser (http:// archaea.ucsc.edu) offers a graphical web-based resource for exploration and discovery within archaeal and other selected microbial genomes.  ...  The genome browser environment maintains the current look-and-feel of the vertebrate UCSC Genome Browser, but also integrates archaeal and bacterial-specific tracks with a few graphic display enhancements  ...  ACKNOWLEDGEMENTS We thank Jim Kent and the Genome Bioinformatics Group of UC Santa Cruz for providing us with excellent assistance in developing the Archaeal Genome Browser.  ... 
doi:10.1093/nar/gkr990 pmid:22080555 pmcid:PMC3245099 fatcat:nbatgfqcjbfqbbwg7a5alvbcyq

Important Databases Related to Genomes [chapter]

K. V. Chaitanya
2019 Genome and Genomics  
Genome databases are the locations, which permits storing, sharing, retrieving and comparison of the information related to the genomes of various individuals and organisms.  ...  In the present chapter, details of the databases related to the genomes of viruses, archaea, bacteria, cell organelle, invertebrates, vertebrates, plants, and human beings are provided in a table format  ...  / Wikipedia List of sequenced archaeal genomes https://en.wikipedia.org/wiki/ List_of_sequenced_archaeal_ genomes UCSC archaeal genome browser Integrated genome browser for archaeal genomes  ... 
doi:10.1007/978-981-15-0702-1_9 fatcat:3w3jpkjxgvhlndeg4plav3oyvm

BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence

Benjamin Hepp, Violette Da Cunha, Florence Lorieux, Jacques Oberto
2021 Bioinformatics  
Existing web-based genome browsers are either too complex for routine use or only provide a subset of the available prokaryotic genomes.  ...  The retrieval of a single gene sequence and context from completely sequenced bacterial and archaeal genomes constitutes an intimidating task for the wet bench biologist.  ...  To overcome these limitations, several web-based genome browsers such as Gbrowse (Stein, 2013) , Ensembl (Yates et al., 2020) and UCSC Genome Browser (Lee et al., 2020) have been developed but are  ... 
doi:10.1093/bioinformatics/btab082 pmid:33532841 fatcat:7h53u543yrdr5kgio7srpgfmky

DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes

Feng Gao, Hao Luo, Chun-Ting Zhang
2012 Nucleic Acids Research  
Consequently, the latest release of DoriC contains oriCs for >1500 bacterial genomes and 81 archaeal genomes, respectively.  ...  However, the origins of replication still remain unknown in a considerably large number of bacterial and archaeal genomes completely sequenced so far.  ...  ACKNOWLEDGEMENTS The authors thank Dr Kurtz for providing the REPuter binaries. They also thank Dr Ren Zhang for critical revision of manuscript.  ... 
doi:10.1093/nar/gks990 pmid:23093601 pmcid:PMC3531139 fatcat:zx77wwfgs5dkfkmhbpfpuepzzi

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

Todd M. Lowe, Patricia P. Chan
2016 Nucleic Acids Research  
results, the most relevant genes in the GtRNAdb and interactive, rich genome context provided by UCSC genome browsers.  ...  High-throughput genome sequencing continues to grow the need for rapid, accurate genome annotation and tRNA genes constitute the largest family of essential, ever-present non-coding RNA genes.  ...  in extensive testing and feedback on the web server interface.  ... 
doi:10.1093/nar/gkw413 pmid:27174935 pmcid:PMC4987944 fatcat:x4grpmkearfebiojfqyyikxmvm

Genome-Wide miRNA Seeds Prediction in Archaea

Shengqin Wang, Yuming Xu, Zuhong Lu
2014 Archaea  
Here, we integrated the phylogenetic information of available archaeal genomes to predict miRNA seeds (typically defined as the 2–8 nucleotides of mature miRNAs) on the genomic scale.  ...  Growing evidence indicates that miRNA genes exist in the archaeal genome, though the functional role of such noncoding RNA remains unclear.  ...  Acknowledgment This work was supported by the National Natural Science Foundation of China (61227803).  ... 
doi:10.1155/2014/671059 pmid:24948879 pmcid:PMC4053300 fatcat:lsonehovo5g53ky6grzetdwr34

GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes

Patricia P. Chan, Todd M. Lowe
2015 Nucleic Acids Research  
Views of tRNA genes in genomic context are provided via direct links to the UCSC genome browsers.  ...  The tRNAscan-SE search tool has become the de facto standard for annotating tRNA genes in genomes, and the Genomic tRNA Database (GtRNAdb) was created as a portal for interactive exploration of these gene  ...  ACKNOWLEDGEMENTS We thank Aaron Cozen for helpful editing of the manuscript. We also thank Andrew Holmes and Aaron Cozen for helping collect MODOMICS data for inclusion in the database.  ... 
doi:10.1093/nar/gkv1309 pmid:26673694 pmcid:PMC4702915 fatcat:yakugldneze67as5bzt6cvczt4

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

P. P. Chan, T. M. Lowe
2009 Nucleic Acids Research  
Direct links for each gene to UCSC eukaryotic and microbial genome browsers provide graphical display of tRNA genes in the context of all other local genetic information.  ...  By far, the major source of new tRNAs is computational identification of genes within newly sequenced genomes.  ...  Alternatively, tRNA genes can now be viewed within the eukaryotic-specific UCSC Genome Browser (5) or similar microbial genome browsers (6) .  ... 
doi:10.1093/nar/gkn787 pmid:18984615 pmcid:PMC2686519 fatcat:jirk2wc2mrbuhemvv4db736nom

Online Resources for Genomic Analysis Using High-Throughput Sequencing

Daniel Blankenberg, James Taylor, Anton Nekrutenko
2015 Cold Spring Harbor Protocols  
Here we describe the use and applications of common file formats for coding and storing genomic data, consider several web-accessible open-source resources for the visualization and analysis of NGS data  ...  As a consequence, several online resources and communities have been developed to assist researchers with both the management and the analysis of sequencing data sets.  ...  ACKNOWLEDGMENTS We, the investigators of this introduction, are lead members of the Galaxy Project team. We thank the other members of the Galaxy Team (E. Afgan, D. Baker, D.B., D. Bouvier, M.  ... 
doi:10.1101/pdb.top083667 pmid:25655493 fatcat:ooet5nofajciro52qzauyo25ka

Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets

Johan Bengtsson, K. Martin Eriksson, Martin Hartmann, Zheng Wang, Belle Damodara Shenoy, Gwen-Aëlle Grelet, Kessy Abarenkov, Anna Petri, Magnus Alm Rosenblad, R. Henrik Nilsson
2011 Antonie van Leeuwenhoek. International Journal of General and Molecular Microbiology  
In addition to being present in the nucleus of eukaryotes and the core genome of prokaryotes, the gene is also found in the mitochondria of eukaryotes and in the chloroplasts of photosynthetic eukaryotes  ...  /metaxa/), an automated software tool to extract full-length and partial SSU sequences from larger sequence datasets and assign 3 them to an archaeal, bacterial, nuclear eukaryote, mitochondrial, or chloroplast  ...  Acknowledgements The Frontiers in Biodiversity Research Centre of Excellence (University of Tartu) and the Platform in Ecotoxicology -From Gene to Ocean (University of Gothenburg) are gratefully acknowledged  ... 
doi:10.1007/s10482-011-9598-6 pmid:21674231 fatcat:sw6e3l3vkraf3o2phy7blp2aha

Transcription Start Site Associated RNAs (TSSaRNAs) Are Ubiquitous in All Domains of Life

Livia S. Zaramela, Ricardo Z. N. Vêncio, Felipe ten-Caten, Nitin S. Baliga, Tie Koide, Szabolcs Semsey
2014 PLoS ONE  
We identified 652 transcripts, of which 179 were shown to be primary transcripts (,7% of the annotated genome).  ...  Here, we provide evidence for existence of TSSaRNAs in several archaeal transcriptomes including: Halobacterium salinarum, Pyrococcus furiosus, Methanococcus maripaludis, and Sulfolobus solfataricus.  ...  Salvanha for extremely helpful discussions on Gaggle Genome Browser usage; to all LaBiSisMi (Laboratório de Biologia Sistêmica de Microorganismos) members specially Sílvia Epifânio and José Vicente Gomes  ... 
doi:10.1371/journal.pone.0107680 pmid:25238539 pmcid:PMC4169567 fatcat:jcbkuvlvuvftpmfs2rr62m5kfy

The BSGatlas: An enhanced annotation of genes and transcripts for the Bacillus subtilis genome with improved information access [article]

Adrian Sven Geissler, Christian Anthon, Enrique González-Tortuero, Line Dahl Poulsen, Thomas Beuchert Kallehauge, Stefan Ernst Seemann, Jeppe Vinther, Jan Gorodkin
2019 bioRxiv   pre-print
The genome of Bacillus subtilis continues to provide exiting genomic insights.  ...  online browser at http://rth.dk/resources/bsgatlas.  ...  The UCSC Archaeal Genome Browser: 2012 update. Nucleic Acids Res 40, D646-D652 (2012). 50. Kent, W. J. BLAT-The BLAST-Like Alignment Tool. Genome Res 12, 656-664 (2002). 51. Robinson, J. T. et al.  ... 
doi:10.1101/807263 fatcat:5fxkvbgbofg23dscplqwxgjnda

Discovery of a minimal form of RNase P in Pyrobaculum

L. B. Lai, P. P. Chan, A. E. Cozen, D. L. Bernick, J. W. Brown, V. Gopalan, T. M. Lowe
2010 Proceedings of the National Academy of Sciences of the United States of America  
Perhaps most surprisingly, Söll and coworkers (12) demonstrated that the archaeal symbiont Nanoarchaeum equitans does not contain any identifiable RNase P genes or detectable RNase P activity, and it appears  ...  sequenced in collaboration with the Joint Genome Institute, providing extensive comparative information.  ...  We are grateful to members of the Joint Genome Institute for making 454 sequencing possible (P. Richardson and J. Bristow for providing resources, and E. Lindquist and N.  ... 
doi:10.1073/pnas.1013969107 pmid:21135215 pmcid:PMC3012483 fatcat:oezh2w7lk5b37ehe733w2x6h6i

The Human Postsynaptic Density Shares Conserved Elements with Proteomes of Unicellular Eukaryotes and Prokaryotes

Richard David Emes, Seth G. N. Grant
2011 Frontiers in Neuroscience  
Acknowledgments supplementARy mAteRiAl The Supplementary Material for this article can be found online at http://www.frontiersin.org/neuroscience/neurogenomics/ paper/10.3389/fnins.2011.00044  ...  In turn these HUGO identifiers could be matched to a total of 4721 transcripts of the March 2006 hg18 human genome build available via the UCSC genome browser.  ...  The whole genome alignments of 44 vertebrate genomes obtained from the UCSC genome browser (see Table S1 in Supplementary Material) were used to generate a hidden Markov model (HMM) for each transcript  ... 
doi:10.3389/fnins.2011.00044 pmid:21503141 pmcid:PMC3071500 fatcat:aexvqv7msnhn7muly3erh36xkm
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