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Tytuł:
DNA sequence features underlying copy number variants
Właściwości sekwencji DNA leżące u podstaw powstawania polimorfizmów liczby kopii
Autorzy:
Barski, P.
Mielczarek, M.
Frąszczak, M.
Szyda, J.
Powiązania:
https://bibliotekanauki.pl/articles/2612539.pdf
Data publikacji:
2019
Wydawca:
Zachodniopomorski Uniwersytet Technologiczny w Szczecinie. Wydawnictwo Uczelniane ZUT w Szczecinie
Tematy:
DNA sequence
copy number variation
genetic analysis
Polish Holstein-Friesian breed
cattle
Źródło:
Acta Scientiarum Polonorum. Zootechnica; 2019, 18, 2; 25-30
1644-0714
Pojawia się w:
Acta Scientiarum Polonorum. Zootechnica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Annotating a non-model plant genome – a study on the narrow-leafed lupin
Autorzy:
Zielezinski, A.
Potarzycki, P.
Ksiazkiewicz, M.
Karlowski, W.M.
Powiązania:
https://bibliotekanauki.pl/articles/80218.pdf
Data publikacji:
2012
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
genome
plant genome
pipeline
software
narrow-leaved lupin
gene annotation system
gene sequence
DNA sequence
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2012, 93, 3
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Comparison of epigenetic changes induced by particular phytohormones and oligonucleotide sequences in flax
Autorzy:
Dzialo, M.
Zuk, M.
Szopa-Skorkowski, J.
Powiązania:
https://bibliotekanauki.pl/articles/951289.pdf
Data publikacji:
2015
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
conference
epigenetic change
phytohormone
oligonucleotide
flax
Linum usitatissimum
DNA sequence
methylation
flavonoids
chalcone synthase
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2015, 96, 1
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
DNA polymorphism in locus D1S80 in Poland. DNA profiling and detection of new alleles by heteroduplex formation between alleles of the same size
Autorzy:
Kwiatkowska, J
Dziechciowska, K
Lisiecka, D
Slomski, R
Powiązania:
https://bibliotekanauki.pl/articles/2046677.pdf
Data publikacji:
1997
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
DNA sequence
polymorphism
Polska
hybridization
Polish population
heteroduplex formation
DNA polymorphism
same size
polymerase chain reaction
allele
distribution
Opis:
We have analysed allele distribution at the highly polymorphic variable number of tandem repeats (VNTR) locus D1S80 (pMCT118) in the Polish population using the, polymerase chain reaction (PCR) technique. Characteristics of the D1S80 locus makes it a very useful marker for population genetic research, genetic linkage studies and forensic identification of individuals. During our routine application of the D1S80 marker to paternity testing in several cases of homozygosity detected by polyacrylamide gel electrophoresis, heteroduplex formation for alleles 18 and 24 was also observed. Direct sequencing of PCR products revealed that alleles 18 and 24 of locus D1S80 actually represent a mixture composed of different sequences. Our observations indicate that identification of some 18 and 24 VNTR alleles based only on size estimated in electrophoretic analyses could lead to errors in paternity testing and DNA profiling.
Źródło:
Journal of Applied Genetics; 1997, 38, 3; 335-341
1234-1983
Pojawia się w:
Journal of Applied Genetics
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Evaluation of methods for Erwinia amylovora detection
Autorzy:
Kaluzna, M.
Pulawska, J.
Mikicinski, A.
Powiązania:
https://bibliotekanauki.pl/articles/1986.pdf
Data publikacji:
2013
Wydawca:
Instytut Ogrodnictwa
Tematy:
Erwinia amylovora
fire blight
real-time polymerase chain reaction
LAMP technique
DNA sequence
detection method
disease control
Źródło:
Journal of Horticultural Research; 2013, 21, 2
2300-5009
Pojawia się w:
Journal of Horticultural Research
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Ancient history of X-ray crystal structure of B-DNA oligomers and its perspective
Autorzy:
Grzeskowiak, K.
Ohishi, H.
Powiązania:
https://bibliotekanauki.pl/articles/80367.pdf
Data publikacji:
2011
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
ancient history
X-ray crystallography
crystal structure
DNA oligomer
DNA binding protein
DNA binding drug
nanotechnology
methylation
nanotube
antitumour agent
DNA restriction
DNA sequence
protein
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2011, 92, 3
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Cloning of the DNA fragments reflecting the open reading frame I and II of the I-18 C gene of Chironomus tentans. VI. The DNA sequencing of the cloned inserts
Autorzy:
Borowicz, B P
Powiązania:
https://bibliotekanauki.pl/articles/66720.pdf
Data publikacji:
1999
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
DNA sequence
pET-3a vector
promoter system
cloning
I-18 C gene
T7 RNA polymerase
Chironomus tentans
polymerase chain reaction
expression
DNA fragment
Opis:
The technology used for the cloning of the open reading frame (ORF) I and II reflecting DNA fragments in regard to the DNA sequencing of the cloned inserts, is presented. The object of the DNA sequencing of the cloned inserts, was to finally confirm and prove the sequence of the inserts as the sequence of the ORF I and II reflecting DNA fragments of the I-18 C gene of Chironomus tentans.
Przedstawiono technologię, zastosowaną do klonowania fragmentów DNA odzwierciedlających otwartą ramę odczytu I i II genu I-18 C Chironomus tentans w zakresie sekwencjonowania sklonowanych wstawek. Celem sekwencjonowania DNA sklonowanych wstawek było ostateczne potwierdzenie i udowodnienie, że sekwencje wklonowanych wstawek były sekwencjami fragmentów DNA odzwierciedlających otwartą ramę odczytu I i II genu I-18 C Chironomus tentans.
Źródło:
Journal of Plant Protection Research; 1999, 39, 1
1427-4345
Pojawia się w:
Journal of Plant Protection Research
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Sequence-specific p53 gene damage by chloroacetaldehyde and its repair kinetics in Escherichia coli
Autorzy:
Kowalczyk, Paweł
Cieśla, Jarosław
Saparbaev, Murat
Laval, Jacques
Tudek, Barbara
Powiązania:
https://bibliotekanauki.pl/articles/1041247.pdf
Data publikacji:
2006
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
chloroacetaldehyde
p53
replication
exocyclic DNA adducts
vinyl chloride
LM-PCR
DNA repair
sequence-specific DNA damage
Opis:
Oxidative stress and certain environmental carcinogens, e.g. vinyl chloride and its metabolite chloroacetaldehyde (CAA), introduce promutagenic exocyclic adducts into DNA, among them 1,N6-ethenoadenine (εA), 3,N4-ethenocytosine (εC) and N2,3-ethenoguanine (εG). We studied sequence-specific interaction of the vinyl-chloride metabolite CAA with human p53 gene exons 5-8, using DNA Polymerase Fingerprint Analysis (DPFA), and identified sites of the highest sensitivity. CAA-induced DNA damage was more extensive in p53 regions which revealed secondary structure perturbations, and were localized in regions of mutation hot-spots. These perturbations inhibited DNA synthesis on undamaged template. We also studied the repair kinetics of CAA-induced DNA lesions in E. coli at nucleotide resolution level. A plasmid bearing full length cDNA of human p53 gene was modified in vitro with 360 mM CAA and transformed into E. coli DH5α strain, in which the adaptive response system had been induced by MMS treatment before the cells were made competent. Following transformation, plasmids were re-isolated from transformed cultures 35, 40, 50 min and 1-24 h after transformation, and further subjected to LM-PCR, using ANPG, MUG and Fpg glycosylases to identify the sites of DNA damage. In adaptive response-induced E. coli cells the majority of DNA lesions recognized by ANPG glycosylase were removed from plasmid DNA within 35 min, while MUG glycosylase excised base modifications only within 50 min, both in a sequence-dependent manner. In non-adapted cells resolution of plasmid topological forms was perturbed, suggesting inhibition of one or more bacterial topoisomerases by unrepaired ε-adducts. We also observed delayed consequences of DNA modification with CAA, manifesting as secondary DNA breaks, which appeared 3 h after transformation of damaged DNA into E. coli, and were repaired after 24 h.
Źródło:
Acta Biochimica Polonica; 2006, 53, 2; 337-347
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
G-DNA – a highly efficient multi-GPU/MPI tool for aligning nucleotide reads
Autorzy:
Frohmberg, W.
Kierzynka, M.
Blazewicz, J.
Gawron, P.
Wojciechowski, P.
Powiązania:
https://bibliotekanauki.pl/articles/200827.pdf
Data publikacji:
2013
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
DNA assembly preprocessing
sequence alignment
GPU computing
Opis:
DNA/RNA sequencing has recently become a primary way researchers generate biological data for further analysis. Assembling algorithms are an integral part of this process. However, some of them require pairwise alignment to be applied to a great deal of reads. Although several efficient alignment tools have been released over the past few years, including those taking advantage of GPUs (Graphics Processing Units), none of them directly targets high-throughput sequencing data. As a result, a need arose to create software that could handle such data as effectively as possible. G-DNA (GPU-based DNA aligner) is the first highly parallel solution that has been optimized to process nucleotide reads (DNA/RNA) from modern sequencing machines. Results show that the software reaches up to 89 GCUPS (Giga Cell Updates Per Second) on a single GPU and as a result it is the fastest tool in its class. Moreover, it scales up well on multiple GPUs systems, including MPI-based computational clusters, where its performance is counted in TCUPS (Tera CUPS).
Źródło:
Bulletin of the Polish Academy of Sciences. Technical Sciences; 2013, 61, 4; 989-992
0239-7528
Pojawia się w:
Bulletin of the Polish Academy of Sciences. Technical Sciences
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Cloning of the Haemophilus influenzae Dam methyltransferase and analysis of its relationship to the Dam methyltransferase encoded by the HP1 phage.
Autorzy:
Bujnicki, Janusz
Radlińska, Monika
Zaleski, Piotr
Piekarowicz, Andrzej
Powiązania:
https://bibliotekanauki.pl/articles/1044039.pdf
Data publikacji:
2001
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
protein structure
sequence specificity
DNA methyltransferase
bioinformatics
molecular evolution
Opis:
In this paper we report cloning and experimental characterization of the DNA adenine methyltransferase (dam) gene from Haemophilus influenzae and comparison of ts product with the Dam protein from the lysogenic phage of H. influenzae, HP1. Molecular modeling of M.HinDam and M.HP1Dam was carried out, providing a framework for a comparative analysis of these enzymes and their close homologs in the tructural context. Both proteins share the common fold and essential cofactor-bind ng and catalytic residues despite overall divergence. However, subtle but significant differences in the cofactor-binding pocket have been identified. Moreover, while M.HinDam seems to contact its target DNA sequence using a number of loops, most of them are missing from M.HP1Dam. Analysis of both MTases suggests that their catalytic activity was derived from a common ancestor, but similar sequence specificities rose by convergence.
Źródło:
Acta Biochimica Polonica; 2001, 48, 4; 969-983
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular identification of Trichoderma strains collected to develop plant growth-promoting and biocontrol agents
Autorzy:
Oskiera, M.
Szczech, M.
Bartoszewski, G.
Powiązania:
https://bibliotekanauki.pl/articles/1976.pdf
Data publikacji:
2015
Wydawca:
Instytut Ogrodnictwa
Tematy:
Trichoderma
strain
molecular identification
biological control agent
multilocus sequence typing
phylogenesis
species identification
DNA isolation
Źródło:
Journal of Horticultural Research; 2015, 23, 1
2300-5009
Pojawia się w:
Journal of Horticultural Research
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Position weight matrix model as a tool for the study of regulatory elements distribution across the DNA sequence
Autorzy:
Jaksik, R.
Rzeszowska-Wolny, J.
Powiązania:
https://bibliotekanauki.pl/articles/229738.pdf
Data publikacji:
2010
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
transcription factors
TFBS
regulation of gene expression
regulatory sequence elements
DNA
position weight matrix
PWM
Opis:
Ab initio methods of DNA regulatory sequence region prediction known as transcription factor binding sites (TFBS) are a very big challenge to modern bioinformatics. Although the currently available methods are not perfect they are fairly reliable and can be used to search for new potential protein-DNA interaction sites. The biggest problem of ab initio approaches is the very high false positive rate of predicted sites which results mainly from the fact that TFBS are very short and highly degenerate. Because of that they can occur by chance every few hundred bases making the task of computational prediction extremely difficult if one aims to reduce the high false positive rate keeping highest possible sensitivity to predict biologically meaningful sequence regions. In this work we present a new application that can be used to predict TFBS regions in very large datasets based on position weight matrix models (PWM’s) using one of the most popular prediction methods. The presented application was used to predict the concentration of TFBS in a set of nearly 2.2 thousand unique sequences of human gene promoter regions. The study revealed that the concentration of TFBS further than 1kbp from the transcription initiation site is constant but it decreases rapidly while getting closer to the transcription initiation site. The decreasing TFBS concentration in the vicinity of genes might result from evolutionary selection which keeps only sites responsible for interactions with proteins being part of a specific regulatory mechanism leading to cells survival.
Źródło:
Archives of Control Sciences; 2010, 20, 4; 491-501
1230-2384
Pojawia się w:
Archives of Control Sciences
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular identification of blast resistance genes in rice genotypes using gene-specific markers
Autorzy:
Al-Daej, M.I.
Ismail, M.
Rezk, A.A.
El-Malky, M.M.
Powiązania:
https://bibliotekanauki.pl/articles/80189.pdf
Data publikacji:
2019
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
molecular identification
resistance gene
rice genotype
Oryza sativa
DNA marker
single-nucleotide polymorphism
simple sequence repeat
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2019, 100, 3
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
A novel approach for identifying DNA repair pathways proteins using an evolutionary approach: Plasmodium falciparum case study
Autorzy:
Milanowska, K.
Wojtczak, J.
Powiązania:
https://bibliotekanauki.pl/articles/80413.pdf
Data publikacji:
2016
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
DNA repair
pathway
ortholog
pipeline
Plasmodium falciparum
proteomics
protein
profile analysis
Hidden Markov model
multiple sequence alignment
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2016, 97, 4
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Transcriptome sequencing: next generation approach to RNA functional analysis
Autorzy:
Zmienko, A.
Jackowiak, P.
Figlerowicz, M.
Powiązania:
https://bibliotekanauki.pl/articles/81137.pdf
Data publikacji:
2011
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
RNA molecule
functional analysis
RNA sequence
transcriptome
isoform
DNA microarray
qualitative change
quantitative change
gene expression
hybridization
oligonucleotide probe
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2011, 92, 4
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Wyświetlanie 1-15 z 21

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