Abstract:
:SPRING (http://algorithm.cs.nthu.edu.tw/tools/SPRING/) is a tool for the analysis of genome rearrangement between two chromosomal genomes using reversals and/or block-interchanges. SPRING takes two or more chromosomes as its input and then computes a minimum series of reversals and/or block-interchanges between any two input chromosomes for transforming one chromosome into another. The input of SPRING can be either bacterial-size sequences or gene/landmark orders. If the input is a set of chromosomal sequences then the SPRING will automatically search for identical landmarks, which are homologous/conserved regions shared by all input sequences. In particular, SPRING also computes the breakpoint distance between any pair of two chromosomes, which can be used to compare with the rearrangement distance to confirm whether they are correlated or not. In addition, SPRING shows phylogenetic trees that are reconstructed based on the rearrangement and breakpoint distance matrixes.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Lin YC,Lu CL,Liu YC,Tang CYdoi
10.1093/nar/gkl169subject
Has Abstractpub_date
2006-07-01 00:00:00pages
W696-9issue
Web Server issueeissn
0305-1048issn
1362-4962pii
34/suppl_2/W696journal_volume
34pub_type
杂志文章abstract::Error-free lesion bypass and error-prone lesion bypass are important cellular responses to DNA damage during replication, both of which require a DNA polymerase (Pol). To identify lesion bypass DNA polymerases, we have purified human Polkappa encoded by the DINB1 gene and examined its response to damaged DNA templates...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.21.4138
更新日期:2000-11-01 00:00:00
abstract::Here we describe a method of labelling short oligonucleotide probes with enzyme without purification or chemical modifications. Biotinylated oligonucleotides as short as 10 nt are coupled with streptavidin-conjugated enzyme, hybridised and detected with enzyme-triggered chemiluminescence. The detection of hybridisatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.2.703
更新日期:1999-01-15 00:00:00
abstract::The abundance and complexity of total poly(A)+RNA of human normal unstimulated lymphocytes, PHA-stimulated and leukemic lymphocytes were examined using the cDNA-poly(A)+ RNA hybridization technique. It was found that in both PHA-stimulated and leukemic lymphocytes the complexity of total poly(A)+RNA is strongly reduce...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.24.7013
更新日期:1981-12-21 00:00:00
abstract::Mammalian DNA (cytosine-5) methyltransferase 1 (DNMT1) is essential for maintenance methylation. Phosphorylation of Ser143 (pSer143) stabilizes DNMT1 during DNA replication. Here, we show 14-3-3 is a reader protein of DNMT1pSer143. In mammalian cells 14-3-3 colocalizes and binds DNMT1pSer143 post-DNA replication. The ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1162
更新日期:2016-02-29 00:00:00
abstract::We have determined the nucleotide sequence of the major species of E. coli tRNASer and of a minor species having the same GGA anticodon. These two tRNAs should recognize the UCC and UCU codons, the most widely used codons for serine in the highly expressed genes of E. coli. The two sequences differ in only one positio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.15.5697
更新日期:1985-08-12 00:00:00
abstract::A specific segment of mitochondrial DNA from 18 people was examined by two methods of direct DNA sequencing. This segment includes a small noncoding region (V) shown before by restriction analysis to exhibit length polymorphism. All 11 of the human mtDNAs previously reported to have a deletion in this region proved to...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.2.529
更新日期:1987-01-26 00:00:00
abstract::DNA synthesis by phage T4 DNA polymerase is arrested at specific sequences in single-stranded DNA templates. To determine whether or not T4 DNA polymerase accessory proteins 32, 44, 45 and 62 eliminated recognition of these arrest sites, unique primer-templates were constructed in which DNA synthesis began at a DNA pr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.8.3343
更新日期:1986-04-25 00:00:00
abstract::To investigate the mechanisms by which oligonucleotides hybridize to target molecules, the binding of two oligodeoxynucleotide probes to RNA targets was measured over a broad range of temperatures. Mutations were then scanned across each DNA/RNA hybrid to map, at single base resolution, sequences important for hybridi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn134
更新日期:2008-05-01 00:00:00
abstract::Systems biologists aim to decipher the structure and dynamics of signaling and regulatory networks underpinning cellular responses; synthetic biologists can use this insight to alter existing networks or engineer de novo ones. Both tasks will benefit from an understanding of which structural and dynamic features of ne...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv595
更新日期:2015-10-30 00:00:00
abstract::A complete physical map of the spinach mitochondrial genome has been established. The entire sequence content of 327 kilobase pairs (kb) is postulated to occur as a single circular molecule. Two directly repeated elements of approximately 6 kb, located on this "master chromosome", are proposed to participate in an int...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.14.5651
更新日期:1986-07-25 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
abstract::We previously showed that mRNAs synthesized from three genes that naturally lack introns contain a portion of their coding sequence, known as a cytoplasmic accumulation region (CAR), which is essential for stable accumulation of the intronless mRNAs in the cytoplasm. The CAR in each mRNA is unexpectedly large, ranging...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1314
更新日期:2013-02-01 00:00:00
abstract::TIAR and HuR are mRNA-binding proteins that play important roles in the regulation of translation. They both possess three RNA recognition motifs (RRMs) and bind to AU-rich elements (AREs), with seemingly overlapping specificity. Here we show using SPR that TIAR and HuR bind to both U-rich and AU-rich RNA in the nanom...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq837
更新日期:2011-02-01 00:00:00
abstract::Large differences in plant genome sizes are mainly due to numerous events of insertions or deletions (indels). The balance between these events determines the evolutionary direction of genome changes. To address the question of what phenomena trigger these alterations, we compared the genomic sequences of two Arabidop...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp183
更新日期:2009-06-01 00:00:00
abstract::A major goal of system biology is the characterization of transcription factors and microRNAs (miRNAs) and the transcriptional programs they regulate. We present Allegro, a method for de-novo discovery of cis-regulatory transcriptional programs through joint analysis of genome-wide expression data and promoter or 3' U...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn1064
更新日期:2009-04-01 00:00:00
abstract::We describe a method for anchoring bacteriophage lambda DNA by one end to gold by Au-biotin-streptavidin-biotin-DNA bonds. DNA anchored to a microfabricated Au line could be aligned and stretched in flow and electric fields. The anchor was shown to resist a force of at least 11 pN, a linkage strong enough to allow DNA...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.3.492
更新日期:1994-02-11 00:00:00
abstract::The enterovirus 71 (EV71) 3Dpol is an RNA-dependent RNA polymerase (RdRP) that plays the central role in the viral genome replication, and is an important target in antiviral studies. Here, we report a crystal structure of EV71 3Dpol elongation complex (EC) at 1.8 Å resolution. The structure reveals that the 5'-end gu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz1170
更新日期:2020-02-20 00:00:00
abstract::Oligodeoxyribonucleotides incorporating non-hydrolyzable dialkyl sulfide linked thymidine dimers (TsT) were synthesized chemically by the solid-phase approach. The sulfide dimer TsT was stable to degradation by snake-venom phosphodiesterase, calf spleen phosphodiesterase, Nuclease P1 and Nuclease S1. Thermal denaturat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.6.1473
更新日期:1993-03-25 00:00:00
abstract::To explain the activation of transcription by a remote enhancer, two models are most often considered, namely looping and scanning. A scanning model, also referred to as 'polymerase entry site' model predicts that for two adjacent promoters the one proximal to an enhancer would be preferentially activated. Preferentia...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.22.8931
更新日期:1989-11-25 00:00:00
abstract::IMGT, the international ImMunoGeneTics database (http://imgt.cines. fr:8104 ), is a high-quality integrated database specialising in Immunoglobulins (Ig), T cell Receptors (TcR) and Major Histocompatibility Complex (MHC) molecules of all vertebrate species, created in 1989 by Marie-Paule Lefranc, Université Montpellie...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.1.219
更新日期:2000-01-01 00:00:00
abstract::Light is a major external factor in regulating seed germination. Photoreceptor phytochrome B (PHYB) plays a predominant role in promoting seed germination in the initial phase after imbibition, partially by repressing phytochrome-interacting factor1 (PIF1). However, the mechanism underlying the PHYB-PIF1-mediated tran...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx283
更新日期:2017-07-07 00:00:00
abstract::In a pilot study on SAGE on Reed-Sternberg cells we have sequenced 1055 tags representing 701 genes. Screening of the GenBank database resulted in the identification of a corresponding gene or EST for 490 of them. For 211 of the tags no homology could be detected. A major problem of the serial analysis of gene express...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.17.e17
更新日期:1999-09-01 00:00:00
abstract::We describe an interactive computer program (ANALYSEQ) that is used from a simple graphics terminal. The main purpose of the program is to determine the function of nucleic acid sequences but it also offers the simpler listing, searching and counting options. It contains methods to locate genes by looking for the effe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.1part2.521
更新日期:1984-01-11 00:00:00
abstract::Saccharomyces cerevisiae chl1 mutants have a significant increase in the rate of chromosome missegregation. CHL1 encodes a 99 kDa predicted protein with an ATP binding site consensus, a putative helix-turn-helix DNA binding motif, and homology to helicases. Using site-directed mutagenesis, I show that mutations that a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.16.3056
更新日期:2000-08-15 00:00:00
abstract::The interaction of antibodies directed toward N6-(delta2-isopentenyl)adenosine, i6Ado, or its nucleotide with related bases, nucleosides, nucleotides and purified tRNAs is described. The selectivity of the antibody preparation was tested in inhibition experiments utilizing a sensitive radioimmunoassay to quantitate th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.9.3439
更新日期:1978-09-01 00:00:00
abstract::We previously showed that histone H4 serine-1 phosphorylation (H4S1ph) is evolutionarily conserved during gametogenesis, and contributes to post-meiotic nuclear compaction and to full completion of sporulation in the yeast Saccharomyces cerevisiae. Previous studies showed that H4S1ph and another modification of the sa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq218
更新日期:2010-08-01 00:00:00
abstract::Discovering which regulatory proteins, especially transcription factors (TFs), are active under certain experimental conditions and identifying the corresponding binding motifs is essential for understanding the regulatory circuits that control cellular programs. The experimental methods used for this purpose are labo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp554
更新日期:2009-09-01 00:00:00
abstract::We have sequenced mouse tRNA genes from two recombinant lambda phage. An 1800 bp sequence from one phage contains 3 tRNA genes, potentially encoding tRNAAsp, tRNAGly, and tRNAGlu, separated by spacer sequences of 587 bp and 436 bp, respectively. The mouse tRNA gene cluster is homologous to a rat sequence (Sekiya et al...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.24.8761
更新日期:1983-12-20 00:00:00
abstract::The SPARC gene 5'flanking sequence has been shown to contain enhancer elements, but also negative control elements immediately upstream of the enhancer elements. Although these 5'enhancer elements are active in F9 and PYS-2 cells, their activities are nullified by the 5'repressor activity. In the present study we have...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.15.3169
更新日期:1997-08-01 00:00:00
abstract::Aryldiazonium salts are shown to be useful as phototriggered structural probes for RNA mapping as well as for footprinting of RNA/protein interaction. In particular the yeast tRNA(Asp)/aspartyl-tRNA synthetase complex is shown to involve the variable loop face and the concave side of the L-shaped nucleic acid bound to...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.1.89
更新日期:1990-01-11 00:00:00