• 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)
  • tandem mass spectro
  • Coding sequences for 16 of the inhibitors were unequivocally associated with specific proteins identified by tandem mass spectrometry (MS/MS) in a previous proteomic analysis of milled white flour from Butte 86. (biomedcentral.com)
  • Our laboratory has previously characterized the proteomes of conditioned media (CM) from 44 cancer cell lines, three near normal cell lines and 11 relevant biological fluids (for example, pancreatic juice and ascites) using multidimensional liquid chromatography tandem mass spectrometry, identifying between 1,000 and 4,000 proteins per cancer site [ 22 - 33 ] (unpublished work). (biomedcentral.com)
  • secretory
  • TRAM2 is a component of the translocon, a gated macromolecular channel that controls the posttranslational processing of nascent secretory and membrane proteins at the endoplasmic reticulum (ER) membrane. (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)
  • Genomics
  • We utilized a genomics approach (i.e., genome sequencing and assembly followed by single nucleotide polymorphism genotyping) to rapidly address these gaps in knowledge. (biomedcentral.com)
  • 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)
  • 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)
  • 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)
  • tissue-specific
  • The present study details a strategy to rapidly identify tissue-specific proteins using bioinformatics. (biomedcentral.com)
  • We developed a strategy that mines six publicly available gene and protein databases for tissue-specific proteins, selects proteins likely to enter the circulation, and integrates proteomic datasets enriched for the cancer secretome to prioritize candidates for further verification and validation studies. (biomedcentral.com)
  • We present a novel strategy using bioinformatics to identify tissue-specific proteins that are potential cancer serum biomarkers. (biomedcentral.com)
  • transcript
  • Based on the transcript assembly and subsequently primer walking, 433 full-length cDNA sequences were successfully generated. (biomedcentral.com)
  • Cloning and sequencing of the 698 nt transcript for CpomGOBP1 resulted in the prediction of a 163 amino acid coding region, and subsequent RT-PCR indicated that the transcripts were mainly expressed in antennae and mouthparts. (usda.gov)
  • Two transcript variants encoding the same protein have been identified for this gene. (wikipedia.org)
  • Despite these difficulties, extensive transcript and protein sequence databases have been generated for human as well as other important model organisms in biology, such as mice and yeast. (wikipedia.org)
  • transiently expressed
  • When transiently expressed, MyoB, MyoC, as well as the common motor domain lacking the tail did not distribute evenly between daughter cells, suggesting some impairment in proper segregation. (rupress.org)
  • receptors
  • The product of this gene, P2Y14 belongs to the family of G-protein coupled receptors, which contains several receptor subtypes with different pharmacological selectivity for various adenosine and uridine nucleotides. (wikipedia.org)
  • The product of this gene, P2Y13, belongs to the family of G-protein coupled receptors. (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)
  • The tool efficiently finds the ORFs for corresponding amino acid sequences and converts them into their single letter amino acid code, and provides their locations in the sequence. (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)
  • molecular
  • Wheat grains accumulate a variety of low molecular weight proteins that are inhibitors of alpha-amylases and proteases and play an important protective role in the grain. (biomedcentral.com)
  • Wheat kernels accumulate a variety of low molecular weight proteins that inhibit amylases and/or proteases from different sources. (biomedcentral.com)
  • This protein has a calculated molecular mass of 47.219kDa. (biochemj.org)
  • In molecular biology, the protein domain SUI1 is a translation initiation factor often found in the fungus, Saccharomyces cerevisiae (Baker's yeast) but it is also found in other eukaryotes and prokaryotes as well as archaea. (wikipedia.org)
  • antigens
  • results have recently been obtained using membrane-spanning protein antigens from the tegument of Schistosoma mansoni . (labome.org)
  • libraries
  • 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)
  • We played significant roles in development of genome maps of cattle, swine, and sheep, and in development of resources such as Bacterial and Yeast Artificial Chromosome libraries, Expressed Sequence Tag databases, and full-length protein- coding mRNA sequences. (usda.gov)
  • This makes it difficult to write programs that can unambiguously determine that two EST libraries were sequenced from the same tissue. (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)
  • translocation
  • It was identified in 1996 through positional cloning of the reciprocal chromosomal t(8;16)(p11;p13) translocation with CREB-binding protein (CBP) associated with a subset of acute myeloid leukemia (AML) (Borrow et al. (springer.com)
  • 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)
  • identification
  • 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)
  • Identification of a human histone acetyltransferase related to monocytic leukemia zinc finger protein. (springer.com)
  • Previous studies have focused on either gene or protein expression databases for the identification of candidates. (biomedcentral.com)
  • 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)
  • tissues
  • 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)
  • abundant
  • Simple sequence repeat (SSR) analysis identified CAG as the most abundant trinucleotide motif, while codon usage analysis revealed that the ten most infrequently used codons in E. tenella are UAU, UGU, GUA, CAU, AUA, CGA, UUA, CUA, CGU and AGU. (biomedcentral.com)
  • 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)
  • Multiple sequence alignments are an essential prerequisite in alignment based phylogenetic reconstructions, because they establish fundamental homology assessments of primary sequence characters. (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)
  • 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)