Abstract：
:Next generation sequencing is widely used to link genetic variants to diseases, and it has massively accelerated the diagnosis and characterization of rare genetic diseases. After initial bioinformatic data processing, the interactive analysis of genome, exome, and panel sequencing data typically starts from lists of genetic variants in VCF format. Medical geneticists filter and annotate these lists to identify variants that may be relevant for the disease under investigation, or to select variants that are reported in a clinical diagnostics setting. We developed VCF.Filter to facilitate the search for disease-linked variants, providing a standalone Java program with a user-friendly interface for interactive variant filtering and annotation. VCF.Filter allows the user to define a broad range of filtering criteria through a graphical interface. Common workflows such as trio analysis and cohort-based filtering are pre-configured, and more complex analyses can be performed using VCF.Filter's support for custom annotations and filtering criteria. All filtering is documented in the results file, thus providing traceability of the interactive variant prioritization. VCF.Filter is an open source tool that is freely and openly available at http://vcffilter.rarediseases.at.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Müller H,Jimenez-Heredia R,Krolo A,Hirschmugl T,Dmytrus J,Boztug K,Bock Cdoi
10.1093/nar/gkx425subject
Has Abstractpub_date
2017-07-03 00:00:00pages
W567-W572issue
W1eissn
0305-1048issn
1362-4962pii
3829196journal_volume
45pub_type
杂志文章abstract：:We have prepared cDNA libraries for amoebae and plasmodia of the acellular slime mould, Physarum polycephalum. Differential screening was used to isolate cell-type-specific cDNA clones (in bacteriophage M13) and both libraries yielded approximately 5% of such sequences. The amoebal- and plasmodial-specific clones were...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.3.933
更新日期：1987-02-11 00:00:00
abstract：:The dominant kanr marker gene plays an important role in gene disruption experiments in budding yeast, as this marker can be used in a variety of yeast strains lacking the conventional yeast markers. We have developed a loxP-kanMX-loxP gene disruption cassette, which combines the advantages of the heterologous kanr ma...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.13.2519
更新日期：1996-07-01 00:00:00
abstract：:In 4M NaCl solutions (dC-dG)n (n = 3,4; approximately 9 mM) exist as a mixture o +/- B and Z forms. The low and high field components of two 31P NMR resonances originating from internal phosphodiester groups are assigned to the GpC and CpG linkages, respectively. Low temperatures stabilize the Z-forms, which completel...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.11.4625
更新日期：1984-06-11 00:00:00
abstract：:The BRENDA enzyme information system (http://www.brenda-enzymes.org/) has developed into an elaborate system of enzyme and enzyme-ligand information obtained from different sources, combined with flexible query systems and evaluation tools. The information is obtained by manual extraction from primary literature, text...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1068
更新日期：2015-01-01 00:00:00
abstract：:Differential display of mRNA is a simple, sensitive and powerful method to identify differentially expressed gene fragments. The main drawback of differential display is the lack of reproducibility and the inability to read and compare complex gels. This issue results from employing unoptimized primer combinations and...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.3.854
更新日期：1998-02-01 00:00:00
abstract：:Argonaute (Ago) proteins function in RNA silencing as components of the RNA-induced silencing complex (RISC). In lower organisms, the small interfering RNA and miRNA pathways diverge due in part to sorting mechanisms that direct distinct small RNA (sRNA) duplexes onto specific Ago-RISCs. However, such sorting mechanis...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku137
更新日期：2014-04-01 00:00:00
abstract：:We have examined the interactions of UvrABC endonuclease with DNA containing the monoadducts of 8-methoxypsoralen (8-MOP) and 4,5',8-trimethylpsoralen (TMP). The UvrA and UvrB proteins were found to form a stable complex on DNA that contains the psoralen monoadducts. Subsequent binding of UvrC protein to this complex ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.12.4957
更新日期：1987-06-25 00:00:00
abstract：:Electrophoretic mobility shift assays (EMSA) were used to define the regions of the INO1 promoter that interact with factors present in extracts prepared from the yeast, Saccharomyces cerevisae. These experiments identified three different types of protein:DNA complexes that assemble with the INO1 promoter. Formation ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.14.3987
更新日期：1991-07-25 00:00:00
abstract：:RNA thermometers control the translation of several heat shock and virulence genes by their temperature-sensitive structural transitions. Changes in the structure and dynamics of MiniROSE RNA, which regulates translation in the temperature range of 20-45°C, were studied by site specifically replacing seven adenine res...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1264
更新日期：2015-01-01 00:00:00
abstract：:GAP-43 is a membrane phosphoprotein that is important for the development and plasticity of neural connections. In undifferentiated PC12 pheochromocytoma cells, GAP-43 mRNA degrades rapidly ( t = 5 h), but becomes stable when cells are treated with nerve growth factor. To identify trans- acting factors that may influe...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.6.1281
更新日期：1997-03-15 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：:ATP-dependent type I topoisomerases from extremely thermophilic archaebacteria--reverse gyrases--drive positive supercoiling of DNA. We showed that reverse gyrase from Desulfurococcus amylolyticus breaks the DNA at specific sites and covalently binds to the 5' end. In 30 out of 31 sites located in pBR322 DNA fragments...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.9.2801
更新日期：1990-05-11 00:00:00
abstract：:Ribosome-inactivating proteins (RIPs) inhibit protein synthesis by enzymatically depurinating a specific adenine residue at the sarcin-ricin loop of the 28S rRNA, which thereby prevents the binding of elongation factors to the GTPase activation centre of the ribosome. Here, we present the 2.2 A crystal structure of tr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn922
更新日期：2009-02-01 00:00:00
abstract：:Protein-RNA interactions play essential roles in a number of regulatory mechanisms for gene expression such as RNA splicing, transport, translation and post-transcriptional control. As the number of available protein-RNA complex 3D structures has increased, it is now possible to statistically examine protein-RNA inter...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl819
更新日期：2006-01-01 00:00:00
abstract：:A novel method for sequence specific double strand DNA cleavage using PNA (peptide nucleic acid) targeting is described. Nuclease S1 digestion of double stranded DNA gives rise to double strand cleavage at an occupied PNA strand displacement binding site, and under optimized conditions complete cleavage can be obtaine...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.9.2103
更新日期：1993-05-11 00:00:00
abstract：:A fiber optic biosensor was used for the fluorimetric detection of T/AT triple-helical DNA formation. The surfaces of two sets of fused silica optical fibers were functionalized with hexaethylene oxide linkers from which decaadenylic acid oligonucleotides were grown in the 3'to 5'and 5'to 3'direction, respectively, us...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.20.4139
更新日期：1997-10-15 00:00:00
abstract：:Conserved segments in DNA or protein sequences are strong candidates for functional elements and thus appropriate methods for computing them need to be developed and compared. We describe five methods and computer programs for finding highly conserved blocks within previously computed multiple alignments, primarily fo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.19.3899
更新日期：1999-10-01 00:00:00
abstract：:In plants, small interfering RNAs (siRNAs) can trigger a silencing signal that may spread within a tissue to adjacent cells or even systemically to other organs. Movement of the signal is initially limited to a few cells, but in some cases the signal can be amplified and travel over larger distances. How far silencing...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1240
更新日期：2011-04-01 00:00:00
abstract：:Genomic DNA of calf thymus contains 1.5 times as much 5-methylcytosine as similar sperm DNA, but the major EcoRI repeat fragment from satellite I of thymus contains ten times as much 5-methylcytosine as the corresponding fragment from sperm DNA. Restriction enzyme analyses of the total DNA and the satellite I fragment...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.18.4537
更新日期：1981-09-25 00:00:00
abstract：:We have compiled the DNA sequence data for E. coli K12 available from the GENBANK and EMBO databases and over a period of several years independently from the literature. We have introduced all available genetic map data and have arranged the sequences accordingly. As far as possible the overlaps are deleted and a tot...
journal_title：Nucleic acids research
pub_type：
doi：10.1093/nar/17.suppl.r283
更新日期：1989-01-01 00:00:00
abstract：:The Kluyveromyces lactis gene encoding the general transcription factor IIB (TFIIB) was isolated from a genomic library by complementation of the cold-sensitive phenotype conferred by a mutation in the SUA7 gene, which encodes TFIIB in Saccharomyces cerevisiae. DNA sequence analysis of the KI-SUA7 gene revealed a 357 ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.15.3413
更新日期：1993-07-25 00:00:00
abstract：:The goal of the present study is to identify genes that respond to iron availability. Suppression subtraction hybridization (SSH) was used to generate cDNA libraries from iron loaded and control human astrocytoma cells (SW1088). The cDNA libraries were screened with antisense cDNA probes obtained from mRNA isolated fr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.8.1802
更新日期：2000-04-15 00:00:00
abstract：:Calf lens messenger fractions have been purified on poly(dT)-cellulose. The purified RNA's have been analyzed as nucleosides by a method which can be used on a micro-scale with highly reproduceble results. Both the 10S and 14S lens mRNA contain poly A sequences. The poly A content found in 14S mRNA cannot account for ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/1.2.245
更新日期：1974-02-01 00:00:00
abstract：:Topoisomerase II is an essential enzyme that is required for virtually every process that requires movement of DNA within the nucleus or the opening of the double helix. This enzyme helps to regulate DNA under- and overwinding and removes knots and tangles from the genetic material. In order to carry out its critical ...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/gkn937
更新日期：2009-02-01 00:00:00
abstract：:Expressed Sequence Tag-based gene expression profiling can be used to discover functionally associated genes on a large scale. Currently available web servers and tools focus on finding differentially expressed genes in different samples or tissues rather than finding co-expressed genes. To fill this gap, we have deve...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki480
更新日期：2005-07-01 00:00:00
abstract：:Mutations in the gene of human RNase T2 are associated with white matter disease of the human brain. Although brain abnormalities (bilateral temporal lobe cysts and multifocal white matter lesions) and clinical symptoms (psychomotor impairments, spasticity and epilepsy) are well characterized, the pathomechanism of RN...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks614
更新日期：2012-09-01 00:00:00
abstract：:DNase I and MPE.Fe (II) footprinting both employ partial cleavage of ligand-protected DNA restriction fragments and Maxam-Gilbert sequencing gel methods of analysis. One method utilizes the enzyme, DNase I, as the DNA cleaving agent while the other employs the synthetic molecule, methidium-propyl-EDTA (MPE). For actin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.16.5555
更新日期：1983-08-25 00:00:00
abstract：:This paper describes a simple program that uses a digitizing device to enter DNA sequences directly from autoradiographs into a computer. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.1part2.499
更新日期：1984-01-11 00:00:00
abstract：:A 12 bp long GCN4-binding, self-complementary duplex DNA d(CATGACGTCATG)(2) has been investigated by NMR spectroscopy to study the structure and dynamics of the molecule in aqueous solution. The NMR structure of the DNA obtained using simulated annealing and iterative relaxation matrix calculations compares quite clos...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.2.499
更新日期：2001-01-15 00:00:00
abstract：:The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of known protein structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and distant evolutionary relationships; the third, fold...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.1.257
更新日期：2000-01-01 00:00:00
