Abstract:
:Phylogenetic analysis and examination of protein domains allow accurate genome annotation and are invaluable to study proteins and protein complex evolution. However, two sequences can be homologous without sharing statistically significant amino acid or nucleotide identity, presenting a challenging bioinformatics problem. We present TreeDomViewer, a visualization tool available as a web-based interface that combines phylogenetic tree description, multiple sequence alignment and InterProScan data of sequences and generates a phylogenetic tree projecting the corresponding protein domain information onto the multiple sequence alignment. Thereby it makes use of existing domain prediction tools such as InterProScan. TreeDomViewer adopts an evolutionary perspective on how domain structure of two or more sequences can be aligned and compared, to subsequently infer the function of an unknown homolog. This provides insight into the function assignment of, in terms of amino acid substitution, very divergent but yet closely related family members. Our tool produces an interactive scalar vector graphics image that provides orthological relationship and domain content of proteins of interest at one glance. In addition, PDF, JPEG or PNG formatted output is also provided. These features make TreeDomViewer a valuable addition to the annotation pipeline of unknown genes or gene products. TreeDomViewer is available at http://www.bioinformatics.nl/tools/treedom/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Alako BT,Rainey D,Nijveen H,Leunissen JAdoi
10.1093/nar/gkl171subject
Has Abstractpub_date
2006-07-01 00:00:00pages
W104-9issue
Web Server issueeissn
0305-1048issn
1362-4962pii
34/suppl_2/W104journal_volume
34pub_type
杂志文章abstract::This article describes recent developments of Europe PMC (http://europepmc.org), the leading database for life science literature. Formerly known as UKPMC, the service was rebranded in November 2012 as Europe PMC to reflect the scope of the funding agencies that support it. Several new developments have enriched Europ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1061
更新日期:2015-01-01 00:00:00
abstract::MicroRNAs are small (approximately 22 nt) RNAs that regulate gene expression and play important roles in both normal and disease physiology. The use of microarrays for global characterization of microRNA expression is becoming increasingly popular and has the potential to be a widely used and valuable research tool. H...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn932
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abstract::From a sarkosyl-insoluble outer membrane fraction prepared from the Helicobacter pylori strain ATCC 43504, 19 proteins could be sequenced N-terminally by Edman degradation. Oligonucleotides were deduced and used for screening of a genomic library. From the isolated genes, five code for different members of a H.pylori ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.16.3325
更新日期:1999-08-15 00:00:00
abstract::The attachment of replicating DNA to a rapidly sedimenting nuclear structure was investigated by digestion with various nucleases. When DNA was gradually removed by DNase I, pulse label incorporated during either 1 min or during 1 hour in the presence of arabinosylcytosine, remained preferentially attached to the nucl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.1.219
更新日期:1979-01-01 00:00:00
abstract::Translation Initiator of Short 5' UTR (TISU) is a unique regulatory element of both transcription and translation initiation. It is present in a sizable number of genes with basic cellular functions and a very short untranslated region (5' UTR). Here, we investigated translation initiation from short 5' UTR mRNAs with...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr484
更新日期:2011-09-01 00:00:00
abstract::The loss of the tumour suppressor E-cadherin (Cdh1) is a key event during tumourigenesis and epithelial-mesenchymal transition (EMT). Transforming growth factor-β (TGFβ) triggers EMT by inducing the expression of non-histone chromatin protein High Mobility Group A2 (HMGA2). We have previously shown that HMGA2, togethe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1293
更新日期:2015-01-01 00:00:00
abstract::The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena), provided by the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI), has for almost forty years continued in its mission to freely archive and present the world's public sequencing data for the benefit of the entire scie...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1028
更新日期:2021-01-08 00:00:00
abstract::Prokaryotes use primed CRISPR adaptation to update their memory bank of spacers against invading genetic elements that have escaped CRISPR interference through mutations in their protospacer target site. We previously observed a trend that nucleotide-dependent mismatches between crRNA and the protospacer strongly infl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky687
更新日期:2018-11-02 00:00:00
abstract::Hepatitis B virus (HBV) replication is initiated by HBV RT binding to the highly conserved encapsidation signal, epsilon, at the 5' end of the RNA pregenome. Epsilon contains an apical stem-loop, whose residues are either totally conserved or show rare non-disruptive mutations. Here we present the structure of the api...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl582
更新日期:2006-01-01 00:00:00
abstract::Understanding the evolutionary and genomic mechanisms responsible for turning the soil-derived saprophytic mycobacteria into lethal intracellular pathogens is a critical step towards the development of strategies for the control of mycobacterial diseases. In this context, Mycobacterium indicus pranii (MIP) is of speci...
journal_title:Nucleic acids research
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doi:10.1093/nar/gks793
更新日期:2012-11-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.14.5547
更新日期:1984-07-25 00:00:00
abstract::RNA-Seq is gradually becoming the standard tool for transcriptomic expression studies in biological research. Although considerable progress has been recorded in the development of statistical algorithms for the detection of differentially expressed genes using RNA-Seq data, the list of detected genes can differ signi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1273
更新日期:2015-02-27 00:00:00
abstract::Expression from the K. pneumoniae nifLA promoter is oxygen sensitive and is also inhibited by the DNA gyrase inhibitor coumermycin A1 under anaerobic growth conditions. The activity of this promoter was found to be highly sensitive to changes in DNA topology in vitro. Transcription was completely dependent on negative...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.21.9933
更新日期:1988-11-11 00:00:00
abstract::In addition to the cap-dependent mechanism, eukaryotic initiation of translation can occur by a cap-independent mechanism which directs ribosomes to defined start codons enabled by internal ribosome entry site (IRES) elements. IRES elements from poliovirus and encephalomyocarditis virus are often used to construct bi-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.16.3327
更新日期:2001-08-15 00:00:00
abstract::Module identification is a frequently used approach for mining local structures with more significance in global networks. Recently, a wide variety of bilayer networks are emerging to characterize the more complex biological processes. In the light of special topological properties of bilayer networks and the accompan...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw679
更新日期:2016-11-16 00:00:00
abstract::It has been proposed that phage lambda site-specific recombination proceeds via two independent strand exchanges: the first exchange forming a Holliday-structure which is then converted into complete recombinant products by the second strand exchange. If this hypothesis is correct, one should be able to trap the putat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.14.6839
更新日期:1988-07-25 00:00:00
abstract::The nucleotide sequences 3' to the translational termination codons in a collection of human genes have been analysed for evidence of a preferred 3' context for natural UAG codons. The aim was to see whether human UAG contexts can be related to the recent demonstration of the effects of 3' context on nonsense suppress...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.1.15
更新日期:1994-01-11 00:00:00
abstract::In synthetic circuits, CRISPR-Cas systems have been used effectively for endpoint changes from an initial state to a final state, such as in logic gates. Here, we use deactivated Cas9 (dCas9) and deactivated Cas12a (dCas12a) to construct dynamic RNA ring oscillators that cycle continuously between states over time in ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa557
更新日期:2020-08-20 00:00:00
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journal_title:Nucleic acids research
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更新日期:2013-01-07 00:00:00
abstract::Adjustable transgene expression is considered key for next-generation molecular interventions in gene therapy scenarios, therapeutic reprogramming of clinical cell phenotypes for tissue engineering and sophisticated gene-function analyses in the post-genomic era. We have designed a portfolio of latest generation self-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnh104
更新日期:2004-07-16 00:00:00
abstract::The cis-requirements for the first editing site in the atp9 mRNA from pea mitochondria were investigated in an in vitro RNA editing system. Template RNAs deleted 5' of -20 are edited correctly, but with decreased efficiency. Deletions between -20 and the edited nucleotide abolish editing activity. Substitution of the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh763
更新日期:2004-08-04 00:00:00
abstract::Chinese hamster genomic DNA sequences from the region downstream of the dihydrofolate reductase (DHFR) gene reported to contain a chromosomal origin of bidirectional DNA replication (OBR-1) were tested for their ability to support autonomous DNA replication in human cells. A 13.3 kilobase fragment containing OBR-1 and...
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更新日期:1992-11-25 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:1997-11-15 00:00:00
abstract::Small regulatory RNAs (sRNAs) from bacterial chromosomes became the focus of research over the past five years. However, relatively little is known in terms of structural requirements, kinetics of interaction with their targets and degradation in contrast to well-studied plasmid-encoded antisense RNAs. Here, we presen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm439
更新日期:2007-01-01 00:00:00
abstract::Helicase loading at a DNA replication origin often requires the dynamic interactions between the DNA helicase and an accessory protein. In E. coli, the DNA helicase is DnaB and DnaC is its loading partner. We used the method of hydrogen/deuterium exchange mass spectrometry to address the importance of DnaB-DnaC comple...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv961
更新日期:2016-01-08 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.suppl.r403
更新日期:1988-01-01 00:00:00
abstract::Partial restriction digestion is used to map restriction sites and the location of genes within yeast artificial chromosomes (YACs). Locus-specific probes are hybridised to the partially digested YAC DNA and the fragments to which they hybridise are compared with the pattern of partial digestion products that include ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.22.4495
更新日期:1996-11-15 00:00:00
abstract::Type IIS restriction endonuclease BtsCI (GGATG 2/0) is a neoschizomer of FokI (GGATG 9/13) and cleaves closer to the recognition sequence. Although M.BtsCI shows 62% amino acid sequence identity to M.FokI, BtsCI and FokI restriction endonucleases do not share significant amino acid sequence similarity. BtsCI belongs t...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2010-03-01 00:00:00
abstract::Recent research hints at an underappreciated complexity in pre-miRNA processing and regulation. Global profiling of pre-miRNA and its potential to increase understanding of the pre-miRNA landscape is impeded by overlap with highly expressed classes of other non coding (nc) RNA. Here, we present a data set excluding th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr903
更新日期:2012-02-01 00:00:00
abstract::The binding of transposase (Tnp) to the specific Tn5 end sequences is the first dedicated reaction during transposition. In this study, comparative DNA-binding analyses were performed using purified full-length Tnp and a C-terminal deletion variant (delta369) that lacks the putative dimerization domain. The shape of t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.19.3790
更新日期:1996-10-01 00:00:00