SEWAL: an open-source platform for next-generation sequence analysis and visualization.

abstract：:R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field l...

journal_title：Nucleic acids research

authors： Vanquelef E,Simon S,Marquant G,Garcia E,Klimerak G,Delepine JC,Cieplak P,Dupradeau FY

更新日期：2011-07-01 00:00:00

abstract：:Despite the extensive use of Saccharomyces cerevisiae as a platform for synthetic biology, strain engineering remains slow and laborious. Here, we employ CRISPR/Cas9 technology to build a cloning-free toolkit that addresses commonly encountered obstacles in metabolic engineering, including chromosomal integration locu...

journal_title：Nucleic acids research

authors： Reider Apel A,d'Espaux L,Wehrs M,Sachs D,Li RA,Tong GJ,Garber M,Nnadi O,Zhuang W,Hillson NJ,Keasling JD,Mukhopadhyay A

更新日期：2017-01-09 00:00:00

abstract：:The three chromosomal DNAs of S. pombe have been fractionated by pulsed field gel electrophoresis. The resulting molecular karyotype will greatly speed gene mapping in this organism, and it indicates that the separation range of the technique extends to DNA molecules as large as 9,000,000 base pairs. ...

journal_title：Nucleic acids research

authors： Smith CL,Matsumoto T,Niwa O,Klco S,Fan JB,Yanagida M,Cantor CR

更新日期：1987-06-11 00:00:00

abstract：:Single-stranded guanosine-rich oligodeoxyribonucleotides (GROs) have a propensity to form quadruplex structures that are stabilized by G-quartets. In addition to intense speculation about the role of G-quartet formation in vivo, there is considerable interest in the therapeutic potential of quadruplex oligonucleotides...

journal_title：Nucleic acids research

authors： Dapić V,Abdomerović V,Marrington R,Peberdy J,Rodger A,Trent JO,Bates PJ

更新日期：2003-04-15 00:00:00

abstract：:The ability to sense and respond to environmental and physiological signals is critical for the survival of the soil-dwelling Gram-positive bacterium Streptomyces coelicolor. Nutrient deprivation triggers the onset of a complex morphological differentiation process that involves the raising of aerial hyphae and format...

journal_title：Nucleic acids research

authors： Haiser HJ,Karginov FV,Hannon GJ,Elliot MA

更新日期：2008-02-01 00:00:00

abstract：:Primer Design Assistant (PDA) is a web interface primer design service combined with thermodynamic theory to evaluate the fitness of primers. It runs in a Linux-Apache-MySQL-PHP structure on a PC equipped with dual CPU (Intel Pentium III 1.4 GHz) and 512 Mb of RAM. A succinct user interface of PDA is accomplished by b...

journal_title：Nucleic acids research

authors： Chen SH,Lin CY,Cho CS,Lo CZ,Hsiung CA

更新日期：2003-07-01 00:00:00

abstract：:Initiation of sporulation in Bacillus subtilis is controlled by several regulators which affect activation by phosphorylation of the key response regulator Spo0A or transcription of Spo0A-P-dependent genes. In vivo overexpression of one of these regulators, sinR , results in suppression of transcription from the Spo0A...

journal_title：Nucleic acids research

authors： Cervin MA,Lewis RJ,Brannigan JA,Spiegelman GB

更新日期：1998-08-15 00:00:00

abstract：:Deep mutational scanning has been used to create high-resolution DNA sequence maps that illustrate the functional consequences of large numbers of point mutations. However, this approach has not yet been applied to libraries of genes created by random circular permutation, an engineering strategy that is used to creat...

journal_title：Nucleic acids research

authors： Atkinson JT,Jones AM,Zhou Q,Silberg JJ

更新日期：2018-07-27 00:00:00

abstract：:In the presence of S-adenosyl methionine the 5' terminal guanosine residue of in vitro synthesized reovirus mRNA becomes methylated at the 2'-OH position. In addition, 7-methyl guanylic acid is condensed covalently at the 5' terminus resulting in the formation of a 5' to 5' triphosphate bridge. Analysis of the 5' term...

journal_title：Nucleic acids research

authors： Faust M,Hastings KE,Millward S

更新日期：1975-08-01 00:00:00

abstract：:The three CD3 genes on human chromosome 11q23 encode proteins (gamma, delta and epsilon) which form part of the antigen receptor on T lymphocytes. All three genes are clustered within 50 kb and are activated approximately contemporaneously during the early stages of T cell ontogeny. In order to pinpoint potential regu...

journal_title：Nucleic acids research

authors： Tunnacliffe A

更新日期：1990-02-11 00:00:00

abstract：:In DNA of the dinoflagellate Crypthecodinium cohnii, 38% of the thymine is replaced by the modified base 5-hydroxymethyluracil, and approximately 3% of the cytosine is replaced by 5-methylcytosine. Both of the modified bases are non-randomly distributed in the DNA. Determinations of 3' nearest neighbors show that HOMe...

journal_title：Nucleic acids research

authors： Steele RE,Rae PM

更新日期：1980-10-24 00:00:00

abstract：:During carcinogenesis, cells are exposed to increased replication stress due to replication fork arrest at sites of DNA lesions and difficult to replicate genomic regions. Efficient fork restart and DNA repair are important for cancer cell proliferation. We previously showed that the ADP-ribosyltransferase PARP10 inte...

journal_title：Nucleic acids research

authors： Schleicher EM,Galvan AM,Imamura-Kawasawa Y,Moldovan GL,Nicolae CM

更新日期：2018-09-28 00:00:00

abstract：:We describe here an energy based computer software suite for narrowing down the search space of tertiary structures of small globular proteins. The protocol comprises eight different computational modules that form an automated pipeline. It combines physics based potentials with biophysical filters to arrive at 10 pla...

journal_title：Nucleic acids research

authors： Jayaram B,Bhushan K,Shenoy SR,Narang P,Bose S,Agrawal P,Sahu D,Pandey V

更新日期：2006-01-01 00:00:00

abstract：:Polyadenylation is a co-transcriptional process that modifies mRNA 3'-ends in eukaryotes. In yeast, CF IA and CPF constitute the core 3'-end maturation complex. CF IA comprises Rna14p, Rna15p, Pcf11p and Clp1p. CF IA interacts with the C-terminal domain of RNA Pol II largest subunit via Pcf11p which links pre-mRNA 3'-...

journal_title：Nucleic acids research

authors： Haddad R,Maurice F,Viphakone N,Voisinet-Hakil F,Fribourg S,Minvielle-Sébastia L

更新日期：2012-02-01 00:00:00

abstract：:Muscleblind-like proteins (MBNLs) are regulators of RNA metabolism. During tissue differentiation the level of MBNLs increases, while their functional insufficiency plays a crucial role in myotonic dystrophy (DM). Deep sequencing of RNA molecules cross-linked to immunoprecipitated protein particles (CLIP-seq) revealed...

journal_title：Nucleic acids research

authors： Konieczny P,Stepniak-Konieczna E,Taylor K,Sznajder LJ,Sobczak K

更新日期：2017-02-28 00:00:00

abstract：:The archaeal exosome is a phosphorolytic 3'-5' exoribonuclease complex. In a reverse reaction it synthesizes A-rich RNA tails. Its RNA-binding cap comprises the eukaryotic orthologs Rrp4 and Csl4, and an archaea-specific subunit annotated as DnaG. In Sulfolobus solfataricus DnaG and Rrp4 but not Csl4 show preference f...

journal_title：Nucleic acids research

authors： Hou L,Klug G,Evguenieva-Hackenberg E

更新日期：2014-11-10 00:00:00

abstract：:It has been proposed that DNA multiply damaged sites (MDS), where more than one moiety in a local region ( approximately 1 helical turn, 10 bp) of the DNA is damaged, are lesions of enhanced biological significance. However, other than indirect measures, there are few analytical techniques that allow direct detection ...

journal_title：Nucleic acids research

authors： Bowman KJ,Pla RL,Guichard Y,Farmer PB,Jones GD

更新日期：2001-10-15 00:00:00

abstract：:Plasmodium falciparum origin recognition complex 1 (ORC1) protein has been implicated in DNA replication and silencing var gene family. However, the mechanism and the domain structure of ORC1 related to the regulation of var gene family are unknown. Here we show that the unique N-terminus of PfORC1 (PfORC1N(1-238)) is...

journal_title：Nucleic acids research

authors： Deshmukh AS,Srivastava S,Herrmann S,Gupta A,Mitra P,Gilberger TW,Dhar SK

更新日期：2012-07-01 00:00:00

abstract：:The Aspergillus nidulans sequence ans1, previously known to enhance transformation frequencies of pyr4-based vectors, was shown to enhance the efficiency of argB and trpC-based vectors. Increased efficiencies could be obtained by constructing vectors containing argB and ans1 or by cotransforming selectable plasmids (c...

journal_title：Nucleic acids research

authors： Cullen D,Wilson LJ,Grey GL,Henner DJ,Turner G,Ballance DJ

更新日期：1987-11-25 00:00:00

abstract：:The thumb subdomain, located in various family B DNA polymerases in the C-terminal region, has been shown in their crystal structures to move upon binding of DNA, changing its conformation to nearly completely wrap around the DNA. It has therefore been involved in DNA binding. In agreement with this, partial proteolys...

journal_title：Nucleic acids research

authors： Truniger V,Lázaro JM,Salas M

更新日期：2004-01-16 00:00:00

abstract：:We report the use of MonoQ FPLC (Fast Protein Liquid Chromatography) for the rapid purification of a novel Type II restriction endonuclease PmaCI, from Pseudomonas maltophila, which recognises the sequence 5'-CAC decreases GTG-3'. The resulting enzyme is free of other nucleases to a level suitable for its characterisa...

journal_title：Nucleic acids research

authors： Walker JN,Dean PD,Saunders JR

更新日期：1986-02-11 00:00:00

abstract：:This work presents the Apo-Holo DataBase (AH-DB, http://ahdb.ee.ncku.edu.tw/ and http://ahdb.csbb.ntu.edu.tw/), which provides corresponding pairs of protein structures before and after binding. Conformational transitions are commonly observed in various protein interactions that are involved in important biological f...

journal_title：Nucleic acids research

authors： Chang DT,Yao TJ,Fan CY,Chiang CY,Bai YH

更新日期：2012-01-01 00:00:00

abstract：:We have developed an information repository named SpliceInfo to collect the occurrences of the four major alternative-splicing (AS) modes in human genome; these include exon skipping, 5'-alternative splicing, 3'-alternative splicing and intron retention. The dataset is derived by comparing the nucleotide and protein s...

journal_title：Nucleic acids research

authors： Huang HD,Horng JT,Lin FM,Chang YC,Huang CC

更新日期：2005-01-01 00:00:00

abstract：:The GWIPS-viz browser (http://gwips.ucc.ie/) is an on-line genome browser which is tailored for exploring ribosome profiling (Ribo-seq) data. Since its publication in 2014, GWIPS-viz provides Ribo-seq data for an additional 14 genomes bringing the current total to 23. The integration of new Ribo-seq data has been auto...

journal_title：Nucleic acids research

authors： Michel AM,Kiniry SJ,O'Connor PBF,Mullan JP,Baranov PV

更新日期：2018-01-04 00:00:00

abstract：:Type I CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas (CRISPR-associated) systems exist in bacterial and archaeal organisms and provide immunity against foreign DNA. The Cas protein content of the DNA interference complexes (termed Cascade) varies between different CRISPR-Cas subtypes. A minima...

journal_title：Nucleic acids research

authors： Dwarakanath S,Brenzinger S,Gleditzsch D,Plagens A,Klingl A,Thormann K,Randau L

更新日期：2015-10-15 00:00:00

abstract：:Starting from a synthetic E. coli promoter with the consensus sequences at -35 and -10 regions, a sequence CAT frequently occurred in the RNA start points of natural promoters was introduced in the downstream of the consensus sequences, and the sequences around the RNA start points as well as the relative positions of...

journal_title：Nucleic acids research

authors： Aoyama T,Takanami M

更新日期：1985-06-11 00:00:00

abstract：:The synthesis of oligonucleotides (ODNs) containing 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine (D) is described, and thermal stability and resistance to enzymatic hydrolysis of the ODNs are compared with ODNs containing 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine (H). The ODNs containing D and the complementary RNA de...

journal_title：Nucleic acids research

authors： Ito T,Ueno Y,Komatsu Y,Matsuda A

更新日期：2003-05-15 00:00:00

abstract：:Synchronous plasmodia of Physarum polycephalum in DNA synthesis were pulse-labelled with [oH]- thymidine for time periods of 15 seconds up to 9 minutes, or given a 30 seconds pulse followed by chase periods of 9 minutes up to 6 hours. Sedimentation analysis in alkaline sucrose gradients revealed at least five species ...

journal_title：Nucleic acids research

authors： Funderud S,Haugli F

更新日期：1975-08-01 00:00:00

abstract：:Ribonuclease III of Escherichia coli is prominently involved in the endoribonucleolytic processing of cell and viral-encoded RNAs. Towards the goal of defining the RNA sequence and structural elements that establish specific catalytic cleavage of RNase III processing signals, this report demonstrates that a 60 nucleot...

journal_title：Nucleic acids research

authors： Chelladurai BS,Li H,Nicholson AW

更新日期：1991-04-25 00:00:00

abstract：:TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff scores and membership in the seed alignment are chosen so that the HMMs can classify numerous proteins according to the...

journal_title：Nucleic acids research

authors： Selengut JD,Haft DH,Davidsen T,Ganapathy A,Gwinn-Giglio M,Nelson WC,Richter AR,White O

更新日期：2007-01-01 00:00:00