• encode
  • Gene transcripts that encode 30 proteins important in the detection of semiochemicals, including sex pheromones, were identified and characterized. (usda.gov)
  • This work provides a source of DNA sequences and the proteins that they encode which are important in the detection of semiochemicals such as pheromones. (usda.gov)
  • A simple gene prediction algorithm for prokaryotes might look for a start codon followed by an open reading frame that is long enough to encode a typical protein, where the codon usage of that region matches the frequency characteristic for the given organism's coding regions. (wikipedia.org)
  • The human and the murine GPR84 ORFs both encode proteins of 396 amino acid residues length with 85% identity and are therefore considered as orthologs. (wikipedia.org)
  • transcriptome
  • This paper describes the generation and characterisation of full-length cDNA sequences from E. tenella second generation merozoites and provides new insights into the E. tenella transcriptome. (biomedcentral.com)
  • Here, we used next-generation sequencing (454 and Illumina) on different tissues from adult and larvae, including chemosensory organs and female ovipositors, to describe the chemosensory transcriptome of S. nonagrioides and identify key molecular components of the pheromone production and detection systems. (ijbs.com)
  • New high-throughput transcriptome sequencing technologies such as RNA-Seq and ChIP-sequencing open opportunities for incorporating additional extrinsic evidence into gene prediction and validation, and allow structurally rich and more accurate alternative to previous methods of measuring gene expression such as expressed sequence tag or DNA microarray. (wikipedia.org)
  • genome sequence
  • The data generated will be useful for the development and validation of diagnostic and control strategies for coccidiosis and will be of value in annotation of the E. tenella genome sequence. (biomedcentral.com)
  • With the bovine draft genome sequence in hand, and development of databases of DNA sequence variation across the genome, we can now turn our attention to leveraging the investment in genome sequence to improve our understanding of the impact and interplay of the genome and the production environment. (usda.gov)
  • Today, with comprehensive genome sequence and powerful computational resources at the disposal of the research community, gene finding has been redefined as a largely computational problem. (wikipedia.org)
  • peptide sequences
  • The output is the predicted peptide sequences in the FASTA format, and a definition line that includes the query ID, the translation reading frame and the nucleotide positions where the coding region begins and ends. (wikipedia.org)
  • Ensembl
  • For example, the RefSeq database contains transcript and protein sequence from many different species, and the Ensembl system comprehensively maps this evidence to human and several other genomes. (wikipedia.org)
  • codling moth
  • Researchers at the USDA-ARS Yakima Agricultural Research Laboratory (Wapato, WA) and Corn Insect and Crop Genetics Research Unit (Ames,IA), and Washington State University (Pullman, WA) have used next generation sequencing to determine gene expression in various codling moth tissues that respond to semiochemicals. (usda.gov)
  • clones
  • More than 15,000 partial sequences were generated from the 5' and 3' ends of clones randomly selected from an E. tenella second generation merozoite full-length cDNA library. (biomedcentral.com)
  • In 1979 teams at Harvard and Caltech extended the basic idea of making DNA copies of mRNAs in vitro to amplifying a library of such in bacterial plasmids In 1982, the idea of selecting random or semi-random clones from such a cDNA library for sequencing was explored by Greg Sutcliffe and coworkers. (wikipedia.org)
  • ORFs
  • In eukaryotic genes with multiple exons, ORFs span intron/exon regions, which may be spliced together after transcription of the ORF to yield the final mRNA for protein translation. (wikipedia.org)
  • Long ORFs are often used, along with other evidence, to initially identify candidate protein-coding regions or functional RNA-coding regions in a DNA sequence. (wikipedia.org)
  • On the other hand, it has been proven that some short ORFs (sORFs) that lack the classical hallmarks of protein-coding genes (both from ncRNAs and mRNAs) can produce functional peptides. (wikipedia.org)
  • homology
  • Multiple sequence alignments are an essential prerequisite in alignment based phylogenetic reconstructions, because they establish fundamental homology assessments of primary sequence characters. (pubmedcentralcanada.ca)
  • Myopodin shows no significant homology to any known protein except synaptopodin. (rupress.org)
  • Genomics
  • Many aspects of structural gene prediction are based on current understanding of underlying biochemical processes in the cell such as gene transcription, translation, protein-protein interactions and regulation processes, which are subject of active research in the various omics fields such as transcriptomics, proteomics, metabolomics, and more generally structural and functional genomics. (wikipedia.org)
  • helminth
  • A helminth protein, or helminthic antigen, is a protein derived from a parasitic worm that causes an immune reaction. (wikipedia.org)
  • Helminth proteins can result in a deregulated response to infection, and are implicated in reduced reactivity to other antigens. (wikipedia.org)
  • Other helminth proteins promote parasite survival in other ways, particularly since parasites must depend on hosts for the supply of essential nutrients. (wikipedia.org)
  • Despite their pathogenic properties, helminth proteins have potential to be co-opted to treat a number of other human diseases. (wikipedia.org)
  • Helminth proteins modulate the immune response of their hosts, but do not suppress it entirely. (wikipedia.org)
  • Additionally, the database can also be used to develop protein targets for new drugs to treat helminth infections. (wikipedia.org)
  • Given the modulatory properties of helminth proteins, it has been suggested that they may be co-opted to successfully treat other human diseases, particularly those associated with auto-immunity disorders. (wikipedia.org)
  • antigens
  • results have recently been obtained using membrane-spanning protein antigens from the tegument of Schistosoma mansoni . (labome.org)
  • species
  • Since this is the first description of GRPs in this species, particular emphasis has been given to the expression pattern of these genes by analyzing their abundance and prevalence in the different cDNA-libraries of the Eucalyptus Genome Sequencing Project Consortium (ForEST). (ufrgs.br)
  • These resources were a key component leading to selection of cattle as a species for complete genome sequencing, which now has opened the door for much more detailed analysis of genome function and evolution among mammals. (usda.gov)
  • A better knowledge of the molecular mechanisms of S. nonagrioides olfaction will contribute to the development of new tools for the control of this species since inhibition/artificial activation of the proteins implicated in the olfactory process would lead to the disruption of its chemical communication. (ijbs.com)
  • Gene finding is one of the first and most important steps in understanding the genome of a species once it has been sequenced. (wikipedia.org)
  • partial
  • Once candidate DNA sequences have been determined, it is a relatively straightforward algorithmic problem to efficiently search a target genome for matches, complete or partial, and exact or inexact. (wikipedia.org)
  • GLUT4
  • Importantly, a number of adipocyte-abundant genes, including GLUT4, hormone sensitive lipase, long-chain fatty acyl-CoA synthase, adipocyte complement-related protein of 30 kDa, and transcription factors CCAAT/enhancer binding protein-α, receptor retinoid X receptor-α, and peroxisome profilerator-activated receptor γ were significantly downregulated by TNF-α treatment. (diabetesjournals.org)
  • Correspondingly, 24-h exposure of 3T3-L1 adipocytes to TNF-α resulted in reduced protein levels of GLUT4 and several insulin signaling proteins, including the insulin receptor, insulin receptor substrate 1 (IRS-1), and protein kinase B (AKT). (diabetesjournals.org)
  • parasite
  • Detailed study of the merozoite stage will support the identification of proteins important to key biological processes in the parasite including host invasion, replication, pathogenicity and the stimulation of host immunity. (biomedcentral.com)
  • When secreted, these proteins may modify the host's immune response in order to promote longevity of the parasite. (wikipedia.org)
  • identification
  • Improvement of the established method for identification of thioredoxin-targeted proteins based on two-dimensional electrophoresis and fluorescence labelling of thiol groups was achieved by application of a highly sensitive Cy5 maleimide dye and large-format two-dimensional gels, resulting in a 10-fold increase in the observed number of labelled protein spots. (biochemj.org)
  • Prolactin-induced protein has also been used for identification and detection of disseminated breast cancer cells. (wikipedia.org)
  • physiological
  • The protein has a physiological function in regulation of water transport mainly in apocrine glands in the axilla, vulva, eyelid and ear canal, serous cells of the submandibular salivary gland, serous cells of the submucosal glands of the bronchi, and accessory lacrimal glands as well as cutaneous eccrine glands. (wikipedia.org)
  • randomly
  • For example, in a randomly generated DNA sequence with an equal percentage of each nucleotide, a stop-codon would be expected once every 21 codons. (wikipedia.org)
  • alignment
  • Methods of alignment masking, which refers to the technique of excluding alignment blocks prior to tree reconstructions, have been successful in improving the signal-to-noise ratio in sequence alignments. (pubmedcentralcanada.ca)
  • However, the lack of formally well defined methods to identify randomness in sequence alignments has prevented a routine application of alignment masking. (pubmedcentralcanada.ca)
  • Alignment masking improves signal-to-noise ratio in multiple sequence alignments prior to phylogenetic reconstruction. (pubmedcentralcanada.ca)
  • Parametric methods of alignment profiling can be easily extended to more complex likelihood based models of sequence evolution which opens the possibility of further improvements. (pubmedcentralcanada.ca)
  • To deal with this problem at the level of sequence alignment, different approaches and alignment software tools have been developed, but despite major advances, alignment quality is still mostly dependent on arbitrary user-given parameters, e.g. gap costs, and inherent features of the data [ 4 , 5 ]. (pubmedcentralcanada.ca)
  • In particular when sequences are highly divergent and/or length variable, sequence alignment and the introduction of gaps become a more and more complex enterprise and can currently not be fully governed by formal algorithms. (pubmedcentralcanada.ca)
  • The major problem is that finding the most accurate alignment parameters in progressive and consistency based alignment approaches is difficult due to the incomplete knowledge of the evolutionary history of sequences and/or heterogeneous processes along sequences [ 6 ]. (pubmedcentralcanada.ca)
  • sequence analyser) ORF Investigator: ORF Investigator is a program which not only gives information about the coding and non coding sequences but also can perform pairwise global alignment of different gene/DNA regions sequences. (wikipedia.org)
  • The pairwise global alignment between the sequences makes it convenient to detect the different mutations, including single nucleotide polymorphism. (wikipedia.org)
  • Sim4 is a nucleotide sequence alignment program akin to BLAST but specifically tailored to DNA to cDNA/EST (Expressed Sequence Tag) alignment (as opposed to DNA-DNA or protein-protein alignment). (wikipedia.org)
  • chromosome
  • Hgpr84 locates to chromosome 12q13.13, and its coding sequence is not interrupted by introns. (wikipedia.org)
  • The protein encoded by this gene forms a heterotrimeric motor complex with kinesin family member 3A and KAP3 (kinesin accessory protein 3) to drive intra-flagellar transport and possibly to aid in chromosome movement during mitosis and meiosis. (wikipedia.org)
  • evolutionary
  • SUI1 is also evolutionary related to hypothetical proteins from Escherichia coli (yciH), Haemophilus influenzae (HI1225) and Methanococcus vannielii. (wikipedia.org)
  • functional
  • In this paper, the structural and functional features of these proteins in Eucalyptus are summarized. (ufrgs.br)
  • This includes protein-coding genes as well as RNA genes, but may also include prediction of other functional elements such as regulatory regions. (wikipedia.org)
  • Determining that a sequence is functional should be distinguished from determining the function of the gene or its product. (wikipedia.org)