• genomes
  • Moreover, by combining the predictions from our recently developed TIS post-processor, ProTISA provides a refined annotation for the public database RefSeq.Furthermore, the database annotates the potential regulatory signals associated with translation initiation at the TIS upstream region.As of July 2007, ProTISA includes 440 microbial genomes with more than 390 000 confirmed TISs. (nih.gov)
  • Here we describe a comprehensive database ProTISA, which collects TIS confirmed through a variety of available evidences for prokaryotic genomes, including Swiss-Prot experiments record, literature, conserved domain hits and sequence alignment between orthologous genes. (nih.gov)
  • Research to find all regulatory regions in the genomes of all sorts of organisms is under way. (wikipedia.org)
  • However, the question was raised, motivated by studies of viral genomes, how to define parameters for gene prediction in a rather short sequence that has no large genomic context. (wikipedia.org)
  • 3, 87-97 Schiex T, Gouzy J, Moisan A, de Oliveira Y. FrameD: A flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences. (wikipedia.org)
  • Borodovsky has made many contributions in the area of development of gene finding algorithms, notably the GeneMark program (1993) that made an impact in the field and was used for annotation of the first completely sequenced genomes of Haemophilus influenzae and Methanococcus jannaschii. (wikipedia.org)
  • Mark Borodovsky homepage at BME Mark Borodovsky research homepage Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training, Genome Research Gene identification in novel eukaryotic genomes by self-training algorithm, Nucleic Acids Research GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses Nucleic Acids Research GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. (wikipedia.org)
  • genes
  • A discrete transition zone organizes the topological and regulatory autonomy of the adjacent tfap2c and bmp7 genes. (nih.gov)
  • Here, we investigate the cis-regulatory organization of the locus containing the Tfap2c and Bmp7 genes in vivo, using a series of engineered chromosomal rearrangements. (nih.gov)
  • While these genes lie adjacent to one another, we demonstrate that they are independently regulated by distinct sets of enhancers, which in turn define non-overlapping regulatory domains. (nih.gov)
  • The two beta-lactamase genes of Streptomyces cacaoi, blaL and blaU, are under the control of the same regulatory system. (uliege.be)
  • It can thus be concluded that the S. cacaoi blaL and blaU genes are controlled by the same regulatory system. (uliege.be)
  • It also provides links to the evidence that supports the proposed TIS to be confirmed: PMID or external database links for IPT TIS, conserved domain search results for CDC-TIS and multiple N-terminal sequence alignments among orthologous genes for HSC TIS.Figure 1. (nih.gov)
  • A regulatory sequence is a segment of a nucleic acid molecule which is capable of increasing or decreasing the expression of specific genes within an organism. (wikipedia.org)
  • Since 2004 models built by the heuristic approach have been used in finding genes in metagenomic sequences. (wikipedia.org)
  • The target sequences and the regulated genes can be listed for each TF, which can be used as benchmark for TFBS recognition tools or as training sets for new TFBS recognition algorithms. (wikipedia.org)
  • Cis-regulatory module (CRM) is a stretch of DNA, usually 100-1000 DNA base pairs in length, where a number of transcription factors can bind and regulate expression of nearby genes and regulate their transcription rates. (wikipedia.org)
  • One cis-regulatory element can regulate several genes, and conversely, one gene can have several cis-regulatory modules.Cis-regulatory modules carry out their function by integrating the active transcription factors and the associated co-factors at a specific time and place in the cell where this information is read and an output is given. (wikipedia.org)
  • In the absence of L-histidine and divalent metal ions or both, HutP does not bind to the hut mRNA, thus allowing the formation of a stem loop terminator structure within the nucleotide sequence located between the hutP and structural genes. (wikipedia.org)
  • In biology and research, short antisense molecules can interact with complementary strands of nucleic acids, modifying expression of genes. (wikipedia.org)
  • DNA strand 1: antisense strand (transcribed to)→ RNA strand (sense) DNA strand 2: sense strand Some regions within a double strand of DNA code for genes, which are usually instructions specifying the order of amino acids in a protein along with regulatory sequences, splicing sites, noncoding introns, and other complicating details. (wikipedia.org)
  • Genome
  • Developed in 1993, original GeneMark was used in 1995 as a primary gene prediction tool for annotation of the first completely sequenced bacterial genome of Haemophilus influenzae, and in 1996 for the first archaeal genome of Methanococcus jannaschii. (wikipedia.org)
  • These algorithms are currently in use in many research labs in the US and abroad as well as at the major sequencing and annotation centers, such as the Broad Institute, DOE Joint Genome Institute and NIH National Center for Biotechnology Information. (wikipedia.org)
  • A transposable element (TE or transposon) is a DNA sequence that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size. (wikipedia.org)
  • Both Watson and Crick strands can be either sense or antisense strands depending on the gene whose sequences are displayed in the genome sequence database. (wikipedia.org)
  • Saccharomyces
  • The analysis suggests complementary strategies for coping with ergosterol depletion by azoles - Saccharomyces imports exogenous ergosterol, Candida exports fluconazole, while Kluyveromyces does neither, leading to extreme sensitivity.This approach revealed significant divergence among regulatory programs associated with fluconazole sensitivity.In future, such approaches might be used to survey a wider range of species, drug concentrations and stimuli to reveal conserved and divergent molecular response pathways. (nih.gov)
  • Genetic
  • An example is the N-glycosylation site motif: Asn, followed by anything but Pro, followed by either Ser or Thr, followed by anything but Pro where the three-letter abbreviations are the conventional designations for amino acids (see genetic code). (wikipedia.org)
  • Regions
  • Previous studies have demonstrated an association between polymorphisms in the regulatory regions of Cyclophilin A (CypA) and susceptibility to both HIV-1 infection and disease progression. (nih.gov)
  • We screened participants of the ACS for the C1604G and A1650G polymorphisms in the regulatory regions of CypA. (nih.gov)
  • Conserved non-coding sequences often contain regulatory regions, and so they are often the subject of these analyses. (wikipedia.org)
  • However, this definition has changed to define cis-regulatory modules as a DNA sequence with transcription factor binding sites which are clustered into modular structures, including -but not limited to- locus control regions, promoters, enhancers, silencers, boundary control elements and other modulators. (wikipedia.org)
  • algorithm
  • Conserved and diverged expression patterns were identified using a novel soft clustering algorithm that concurrently clusters data from all species while incorporating sequence orthology. (nih.gov)
  • The algorithm introduced inhomogeneous three-periodic Markov chain models of protein-coding DNA sequence that became standard in gene prediction as well as Bayesian approach to gene prediction in two DNA strands simultaneously. (wikipedia.org)
  • electrophoresis
  • Western analysis and immunohistochemistry were used to detect and confirm the protein expression, and hyaluronic acid substrate gel electrophoresis analyzed its hyaluronidase activity. (nih.gov)
  • Electrophoretic sequencing gels or capillary electrophoresis have been successful in analyzing footprinting of fluorescent tagged fragments. (wikipedia.org)
  • experiments
  • Experiments using heterologous gene fusions showed that all of the effects leading to increased expression of CIT2 were transcriptionally controlled through 5'-flanking CIT2 DNA sequences. (denigma.de)
  • Analysis
  • Radioactivity has been traditionally used to label DNA fragments for footprinting analysis, as the method was originally developed from the Maxam-Gilbert chemical sequencing technique. (wikipedia.org)
  • database
  • Furthermore, the database annotates the potential regulatory signals associated with translation initiation at the TIS upstream region. (nih.gov)
  • characteristic
  • The BlaA DNA binding-site was further restricted to a 30-bp sequence containing a T-N11-A motif, a characteristic of LysR-type promoters. (uliege.be)
  • TESS also provides a program for the identification of cis-regulatory modules (CRMs, characteristic combinations of TFBSs), which uses TRANSFAC matrices. (wikipedia.org)
  • Thus gene-regulation functions (GRF) provide a unique characteristic of a cis-regulatory module (CRM), relating the concentrations of transcription factors (input) to the promoter activities (output). (wikipedia.org)
  • Depending
  • Depending on how close together the parts of the sequence are that are self-complementary, the strand may form hairpin loops, junctions, bulges or internal loops. (wikipedia.org)
  • Unfortunately no available agents meet all of these standards, so an appropriate agent can be chosen, depending on your DNA sequence and ligand of interest. (wikipedia.org)
  • Molecular
  • vague] Molecular biologists call a single strand of DNA, sense (or positive (+)) if an RNA version of the same sequence is translated or translatable into protein. (wikipedia.org)
  • consensus sequence
  • See also consensus sequence. (wikipedia.org)
  • Usually, however, the first letter is I, and both [RK] choices resolve to R. Since the last choice is so wide, the pattern IQxxxRGxxxR is sometimes equated with the IQ motif itself, but a more accurate description would be a consensus sequence for the IQ motif. (wikipedia.org)
  • promoter
  • These include, but are not limited to: CACGTT sequence 20 bp upstream of the mouse Period2 (PER2) gene and regulates its expression CAGCTT sequence found within the MyoD core enhancer CACCTCGTGAC sequence in the proximal promoter region of human and rat APOE, which is a protein component of lipoproteins. (wikipedia.org)
  • The original definition presented cis-regulatory modules as enhancers of cis-acting DNA, which increased the rate of transcription from a linked promoter. (wikipedia.org)
  • organisms
  • This evolutionary conservation means that the specific sequence of this domain is important for the survival of most species throughout the spectrum of living organisms. (wikipedia.org)
  • localization
  • This localization is mediated by isoform-specific 3'-untranslated sequences (zipcodes) and can be inhibited by antizipcode oligodeoxynucleotides (ODNs) (Kislauskis, E.H., X.-C. Zhu, and R.H. Singer. (umassmed.edu)
  • Binding of a TF to a genomic site is documented by specifying the localization of the site, its sequence and the experimental method applied. (wikipedia.org)
  • determines
  • The design of cis-regulatory modules is such that transcription factors and epigenetic modifications serve as inputs, and the output of the module is the command given to the transcription machinery, which in turn determines the rate of gene transcription or whether it is turned on or off. (wikipedia.org)
  • Within the assumption of the Boolean logic, principles guiding the operation of these modules includes the design of the module which determines the regulatory function. (wikipedia.org)
  • denotes
  • A string of characters drawn from the alphabet and enclosed in braces (curly brackets) denotes any amino acid except for those in the string. (wikipedia.org)
  • complementary
  • In nature complementarity is the base principle of DNA replication and transcription as it is a property shared between two DNA or RNA sequences, such that when they are aligned antiparallel to each other, the nucleotide bases at each position in the sequences will be complementary, much like looking in the mirror and seeing the reverse of things. (wikipedia.org)
  • This complementary base pairing allows cells to copy information from one generation to another and even find and repair damage to the information stored in the sequences. (wikipedia.org)