Automating the determination of open reading frames in genomic sequences using the Web service techniques - A case study using SARS coronavirus

2004 ◽  
Author(s):  
P.H.-M. Chang ◽  
Von-Wun Soo ◽  
Tai-Yu Chen ◽  
Wei-Shen Lai ◽  
Shiun-Cheng Su ◽  
...  
Keyword(s):  
Web Service ◽  
Open Reading Frames ◽  
Genomic Sequences ◽  
Sars Coronavirus ◽  
Reading Frames ◽  
The Web

scholarly journals Application of Serial Analysis of Gene Expression to the Study of the Gene Expression Profile ofLeishmania infantum chagasiPromastigote

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Adelino Soares Lima Neto ◽  
Osvaldo Pompílio de Melo Neto ◽  
Carlos Henrique Nery Costa
Keyword(s):  
Gene Expression ◽  
Life Cycle ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Leishmania Infantum ◽  
Open Reading Frames ◽  
Genomic Sequences ◽  
Coding Sequences ◽  
Key Genes ◽  
Reading Frames

This study describes the application of the LongSAGE methodology to study the gene expression profile in promastigotes ofLeishmania infantum chagasi. A tag library was created using the LongSAGE method and consisted of 14,208 tags of 17 bases. Of these, 8,427 (59.3%) were distinct. BLAST research of the 1,645 most abundant tags showed that 12.8% of them identified the coding sequences of genes, while 82% (1,349/1,645) identified one or more genomic sequences that did not correspond with open reading frames. Only 5.2% (84/1,645) of the tags were not aligned to any position in theL. infantum genome. The UTR size ofLeishmaniaand the lack of CATG sites in some transcripts were decisive for the generation of tags in these regions. Additional analysis will allow a better understanding of the expression profile and discovering the key genes in this life cycle.

scholarly journals Genetic and Biochemical Characterization of a Novel Monoterpene ɛ-Lactone Hydrolase from Rhodococcus erythropolis DCL14

2001 ◽  
Vol 67 (2) ◽  
pp. 733-741 ◽  
Author(s):  
Cécile J. B van der Vlugt-Bergmans ◽  
Mariët J. van der Werf
Keyword(s):  
Ring Opening ◽  
Biochemical Characterization ◽  
Rhodococcus Erythropolis ◽  
Open Reading Frames ◽  
Apparent Homogeneity ◽  
Terminal Amino ◽  
Acyl Coenzyme A ◽  
Reading Frames

ABSTRACT A monoterpene ɛ-lactone hydrolase (MLH) from Rhodococcus erythropolis DCL14, catalyzing the ring opening of lactones which are formed during degradation of several monocyclic monoterpenes, including carvone and menthol, was purified to apparent homogeneity. It is a monomeric enzyme of 31 kDa that is active with (4R)-4-isopropenyl-7-methyl-2-oxo-oxepanone and (6R)-6-isopropenyl-3-methyl-2-oxo-oxepanone, lactones derived from (4R)-dihydrocarvone, and 7-isopropyl-4-methyl-2-oxo-oxepanone, the lactone derived from menthone. Both enantiomers of 4-, 5-, 6-, and 7-methyl-2-oxo-oxepanone were converted at equal rates, suggesting that the enzyme is not stereoselective. Maximal enzyme activity was measured at pH 9.5 and 30°C. Determination of the N-terminal amino acid sequence of purified MLH enabled cloning of the corresponding gene by a combination of PCR and colony screening. The gene, designated mlhB(monoterpene lactone hydrolysis), showed up to 43% similarity to members of the GDXG family of lipolytic enzymes. Sequencing of the adjacent regions revealed two other open reading frames, one encoding a protein with similarity to the short-chain dehydrogenase reductase family and the second encoding a protein with similarity to acyl coenzyme A dehydrogenases. Both enzymes are possibly also involved in the monoterpene degradation pathways of this microorganism.

scholarly journals A diadenosine 5',5''-P1P4 tetraphosphate (Ap4A) hydrolase from Arabidopsis thaliana that is activated preferentially by Mn2+ ions.

2008 ◽  
Vol 55 (1) ◽  
pp. 151-160 ◽  
Author(s):  
Blanka Szurmak ◽  
Aleksandra Wysłouch-Cieszyńska ◽  
Małgorzata Wszelaka-Rylik ◽  
Wojciech Bal ◽  
Marta Dobrzańska
Keyword(s):  
Arabidopsis Thaliana ◽  
Binding Constants ◽  
Open Reading Frames ◽  
Titration Calorimetry ◽  
Sequence Homologies ◽  
Dna Replication And Repair ◽  
Model Plant Arabidopsis Thaliana ◽  
Reading Frames

Asymmetrical diadenosine 5',5''-P(1)P(4) tetraphosphate (Ap(4)A) hydrolases are key enzymes controlling the in vivo concentration of Ap(4)A--an important signaling molecule involved in regulation of DNA replication and repair, signaling in stress response and apoptosis. Sequence homologies indicate that the genome of the model plant Arabidopsis thaliana contains at least three open reading frames encoding presumptive Ap(4)A hydrolases: At1g30110, At3g10620, and At5g06340. In this work we present efficient overexpression and detailed biochemical characteristics of the AtNUDX25 protein encoded by the At1g30110 gene. Aided by the determination of the binding constants of Mn(Ap(4)A) and Mg(Ap(4)A) complexes using isothermal titration calorimetry (ITC) we show that AtNUDX25 preferentially hydrolyzes Ap(4)A in the form of a Mn(2+) complex.

scholarly journals uORF-Tools – Workflow for the determination of translation-regulatory upstream open reading frames

2018 ◽  
Author(s):  
Anica Scholz ◽  
Florian Eggenhofer ◽  
Rick Gelhausen ◽  
Björn Grüning ◽  
Kathi Zarnack ◽  
...  
Keyword(s):  
Ribosome Profiling ◽  
Open Reading Frames ◽  
Annotation File ◽  
Inhibitory Effects ◽  
Protein Coding ◽  
Reading Frame ◽  
Upstream Open Reading Frames ◽  
Induced Changes ◽  
Reading Frames

AbstractRibosome profiling (ribo-seq) provides a means to analyze active translation by determining ribosome occupancy in a transcriptome-wide manner. The vast majority of ribosome protected fragments (RPFs) resides within the protein-coding sequence of mRNAs. However, commonly reads are also found within the transcript leader sequence (TLS) (aka 5’ untranslated region) preceding the main open reading frame (ORF), indicating the translation of regulatory upstream ORFs (uORFs). Here, we present a workflow for the identification of translation-regulatory uORFs. Specifically, uORF-Tools identifies uORFs within a given dataset and generates a uORF annotation file. In addition, a comprehensive human uORF annotation file, based on 35 ribo-seq files, is provided, which can serve as an alternative input file for the workflow. To assess the translation-regulatory activity of the uORFs, stimulus-induced changes in the ratio of the RPFs residing in the main ORFs relative to those found in the associated uORFs are determined. The resulting output file allows for the easy identification of candidate uORFs, which have translation-inhibitory effects on their associated main ORFs. uORF-Tools is available as a free and open Snakemake workflow at https://github.com/Biochemistry1-FFM/uORF-Tools. It is easily installed and all necessary tools are provided in a version-controlled manner, which also ensures lasting usability. uORF-Tools is designed for intuitive use and requires only limited computing times and resources.

scholarly journals uORF-Tools—Workflow for the determination of translation-regulatory upstream open reading frames

PLoS ONE ◽  
2019 ◽  
Vol 14 (9) ◽  
pp. e0222459 ◽  
Author(s):  
Anica Scholz ◽  
Florian Eggenhofer ◽  
Rick Gelhausen ◽  
Björn Grüning ◽  
Kathi Zarnack ◽  
...  
Keyword(s):  
Open Reading Frames ◽  
Upstream Open Reading Frames ◽  
Reading Frames

scholarly journals A New Class of Genetic Element, Staphylococcus Cassette Chromosome mec, Encodes Methicillin Resistance in Staphylococcus aureus

2000 ◽  
Vol 44 (6) ◽  
pp. 1549-1555 ◽  
Author(s):  
Y. Katayama ◽  
T. Ito ◽  
K. Hiramatsu
Keyword(s):  
Staphylococcus Aureus ◽  
Methicillin Resistance ◽  
Open Reading Frames ◽  
Multicopy Plasmid ◽  
Sequence Determination ◽  
New Class ◽  
New Family ◽  
Partial Homology ◽  
Reading Frames

ABSTRACT We have previously shown that the methicillin-resistance genemecA of Staphylococcus aureus strain N315 is localized within a large (52-kb) DNA cassette (designated the staphylococcal cassette chromosome mec[SCCmec]) inserted in the chromosome. By sequence determination of the entire DNA, we identified two novel genes (designated cassette chromosome recombinase genes [ccrAand ccrB]) encoding polypeptides having a partial homology to recombinases of the invertase/resolvase family. The open reading frames were found to catalyze precise excision of the SCCmec from the methicillin-resistant S. aureuschromosome and site-specific as well as orientation-specific integration of the SCCmec into the S. aureuschromosome when introduced into the cells as a recombinant multicopy plasmid. We propose that SCCmec driven by a novel set of recombinases represents a new family of staphylococcal genomic elements.

scholarly journals Annotating the Mycobacterium avium Genome: A Project in Bioinformatics

2004 ◽  
Vol 7 (2) ◽  
Author(s):  
David D. Shersher ◽  
Maksim Kirtsman ◽  
Mikael Katz-Lavigne ◽  
Marcel A. Behr ◽  
Makeda Semret
Keyword(s):  
Biological Sciences ◽  
Mycobacterium Avium ◽  
Open Reading Frames ◽  
Genomic Research ◽  
Mycobacterial Species ◽  
Bioinformatic Tools ◽  
Homologous Sequences ◽  
Efficient Processing ◽  
Reading Frames

Bioinformatic tools facilitate efficient processing and formatting of experimental data and are becoming essential to research in the biological sciences. Whole genome sequencing projects, combined with DNA microarray technology, have allowed genomic comparisons between and within species of microorganisms. The genome of Mycobacterium avium subsp. avium (MAA) has been sequenced by The Institute for Genomic Research (TIGR), but a final and annotated version has not yet been made available. The goal of this project was to annotate the sequence of MAA as a foundation for microarray-based genomic comparisons. We used software to identify and predict open reading frames (ORFs) present in this organism. The ORFs were then compared to those catalogued in two large, online genetic databases for other microorganisms and matched to homologous sequences, allowing the determination of putative functions for each predicted gene. The genome of MAA was determined to contain 4480 genes, the majority of which are homologous to genes found in other Mycobacterial species.

WSMoD

2010 ◽  
pp. 16-44
Author(s):  
M. Comerio ◽  
F. De Paoli ◽  
S. Grega ◽  
A. Maurino ◽  
Carlo Batini
Keyword(s):  
Web Services ◽  
Web Service ◽  
Common Knowledge ◽  
Effective Means ◽  
Service Design ◽  
General Knowledge ◽  
Customer Requirements ◽  
The Web ◽  
Independent Model

Web services are increasingly used as an effective means to create and streamline processes and collaborations among governments, businesses, and citizens. As the number of available web services is steadily increasing, there is a growing interest in providing methodologies that address the design of web services according to specific qualities of service (QoS) rather than functional descriptions only. This chapter presents WSMoD (Web Services MOdeling Design), a methodology that explicitly addresses this issue. Furthermore, it exploits general knowledge available on services, expressed by ontologies describing services, their qualities, and the context of use, to help the designer in expressing service requirements in terms of design artifacts. Ontologies are used to acquire and specialize common knowledge among the entities involved in service design, and to check the consistency of the web service model with constraints defined by provider and customer requirements. To improve the effectiveness of the process, the authors propose a Platform Independent Model that includes the description of specific context of service provision, without considering implementation details. The discussion of a QoS-based web service design within a real case study bears evidence of the potentials of WSMoD.

Phylogenetics and evolution of potato virus V: another potyvirus that originated in the Andes

Plant Disease ◽  
2021 ◽  
Author(s):  
Segundo Fuentes ◽  
Adrian J Gibbs ◽  
Ian Adams ◽  
Mohammad Hajizadeh ◽  
Jan Kreuze ◽  
...  
Keyword(s):  
South America ◽  
Potato Virus ◽  
Potato Virus Y ◽  
Open Reading Frames ◽  
Genomic Sequences ◽  
Andean Region ◽  
The Andes ◽  
Columbian Exchange ◽  
Reading Frames ◽  
Complete Genomic

Potato virus V (PVV) causes a disease of potato (Solanum tubersosum) in South and Central America, Europe and the Middle East. We report here the complete genomic sequences of 42 new PVV isolates from the potato’s Andean domestication centre in Peru, and of eight historical or recent isolates from Europe. When the principal open reading frames (ORFs) of these genomic sequences together with those of nine previously published genomic sequences were analysed, only two from Peru and one from Iran were found to be recombinant. The phylogeny of the 56 non-recombinant ORF sequences showed that the PVV population has two major phylogroups, one of which forms three minor phylogroups (A1-A3) of isolates, all of which are only found in the Andean region of South America (Peru and Colombia), and the other forms two minor phylogroups, a basal one of Andean isolates (A4) that is paraphyletic to a crown cluster containing all the isolates found outside South America (World). This suggests that PVV originated in the Andean region with only one minor phylogroup spreading elsewhere in the world. In minor phylogroups A3 and A4, there were subclades on long branches containing isolates from S. phureja evolving more rapidly than the others, and these interfered with dating calculations. Although no temporal signal was directly detected among the dated non-recombinant sequences, PVV and potato virus Y (PVY) are from the same potyvirus lineage and are ecologically similar, so “sub-tree dating” was done using a single maximum-likelihood phylogeny of PVV and PVY sequences, and PVY’s well-supported 157 CE “time to most common recent ancestor” was extrapolated to date that of PVV as 29 BCE. Thus the independent historical coincidences supporting the datings of the PVV and PVY phylogenies are the same; PVV arose at least 2,000 years ago in the Andes, and was taken to Europe during the Columbian Exchange, where it diversified around 1853 CE soon after the European potato late blight pandemic. PVV is likely to be more widespread than currently realised, and of biosecurity relevance for world regions that have not yet recorded its presence.

scholarly journals Data Mining in Web Services Discovery and Monitoring

2011 ◽  
pp. 270-289 ◽  
Author(s):  
Richi Nayak
Keyword(s):  
Data Mining ◽  
Web Services ◽  
Web Service ◽  
Service Discovery ◽  
Data Mining Technique ◽  
Service Usage ◽  
Clustering Data ◽  
The Web ◽  
Usage Data

The business needs, the availability of huge volumes of data and the continuous evolution in Web services functions derive the need of application of data mining in the Web service domain. This article recommends several data mining applications that can leverage problems concerned with the discovery and monitoring of Web services. This article then presents a case study on applying the clustering data mining technique to the Web service usage data to improve the Web service discovery process. This article also discusses the challenges that arise when applying data mining to Web services usage data and abstract informat

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