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The UCSC Archaeal Genome Browser
2006
Nucleic Acids Research
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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
2011
Nucleic Acids Research
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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]
2019
Genome and Genomics
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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
2021
Bioinformatics
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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
2012
Nucleic Acids Research
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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
2016
Nucleic Acids Research
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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
2014
Archaea
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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
2015
Nucleic Acids Research
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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
2009
Nucleic Acids Research
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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
2015
Cold Spring Harbor Protocols
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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
2011
Antonie van Leeuwenhoek. International Journal of General and Molecular Microbiology
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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
2014
PLoS ONE
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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]
2019
bioRxiv
pre-print
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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
2010
Proceedings of the National Academy of Sciences of the United States of America
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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
2011
Frontiers in Neuroscience
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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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