• Prediction of the coding sequences of unidentified human genes. (nih.gov)
  • This is then a gene-centric assembly where the goal is to assemble reads into contigs for a family of orthologous genes. (biomedcentral.com)
  • Using published synthetic community metagenome sequencing reads and a set of 41 gene families, we show that the performance of this approach compares favorably with that of full-featured assemblers and that of a recently published HMM-based gene-centric assembler, both in terms of the number of reference genes detected and of the percentage of reference sequence covered. (biomedcentral.com)
  • A gene-centric assembly for a family of orthologous genes F is the assembly of all reads associated with F . One approach to this is simply to run an existing assembly tool on the reads. (biomedcentral.com)
  • In our evaluation, we find that the MEGAN assembler performs best in terms of the percentage of reference genes covered and percentage of reference gene sequences detected. (biomedcentral.com)
  • However, several open questions still remain, such as, how these tandem repeats appeared in the evolutionary path or how they have evolved in orthologous genes of related organisms. (inderscience.com)
  • In this paper, we present a computational solution that facilitates comparative studies of orthologous genes from various organisms. (inderscience.com)
  • HACNSs are disproportionately associated with genes involved in neuronal migration, adhesion, axon guidance and synapse formation, suggesting that cis-regulatory changes in human evolution may have contributed to changes in brain development and function. (yale.edu)
  • Our aim was to clone and sequence the cDNA of the BB diabetes prone (DP) and diabetes resistant (DR) alleles of all seven Gimap genes in the congenic DR. lyp rat line with 2 Mb of BB DP DNA introgressed onto the DR genetic background. (hindawi.com)
  • The fact that the Gimap genes are located together in a tight cluster on RNO4 (and in conserved synteny with many other species), combined with their sequence similarities, suggests the possibility that the proteins carry out similar function. (hindawi.com)
  • Here, we present a phylogenomics-based approach for the identification of orthologous and paralogous genes in human, mouse, fly, and worm, which forms the foundation of the comparative analyses of the modENCODE and mouse ENCODE projects. (biorxiv.org)
  • We study a median of 16,101 genes across 2 mammalian genomes (human, mouse), 12 Drosophila genomes, 5 Caenorhabditis genomes, and an outgroup yeast genome, and demonstrate that accurate inference of evolutionary relationships and events across these species must account for frequent gene-tree topology errors due to both incomplete lineage sorting and insufficient phylogenetic signal. (biorxiv.org)
  • Furthermore, we show that integration of two separate phylogenomic pipelines yields increased accuracy, suggesting that their sources of error are independent, and finally, we leverage the resulting annotation of homologous genes to study the functional impact of gene duplication and loss in the context of rich gene expression and functional genomic datasets of the modENCODE, mouse ENCODE, and human ENCODE projects. (biorxiv.org)
  • The very premise of using model organisms to inform human biology relies on the fact that many biological processes, and the underlying genomic elements that encode them, are frequently conserved across large evolutionary distances, especially for protein-coding genes. (biorxiv.org)
  • To inform each other and human, model organism studies require a complete map of functionally-equivalent genes and processes across species, in order to facilitate mapping of biological and experimental findings across species, but such maps are extremely difficult to obtain experimentally. (biorxiv.org)
  • For any given set of species, gene families are created by first identifying all the genes in all species and then clustering them based on their sequence similarities. (biorxiv.org)
  • Curved links encode sequence similarity and outer data tracks represent consensus similarity statistics and orthologous genes. (bcgsc.ca)
  • Based on human-mouse evolutionarily conserved transcription factor binding sites (TFBSs) in 76600 conserved blocks for 5169 genes, we compiled the human transcriptional connections into a matrix, and examined the number of FFC appearances in comparison with randomized networks. (biomedcentral.com)
  • We compiled the human transcriptional connections into a connection matrix, based on the computationally identified human-mouse conserved TF binding sites (TFBSs) of 82 well-annotated TFs in 76600 conserved blocks located within the 8-kb upstream sequences of 5169 human genes that were stringent orthologs to mouse counterpart genes. (biomedcentral.com)
  • DNA sequencing of 623 genes with known or potential relationships to cancer revealed more than 1,000 somatic mutations across the samples. (kb.se)
  • These data provide evidence of somatic mutations in primary lung adenocarcinoma for several tumour suppressor genes involved in other cancers--including NF1, APC, RB1 and ATM--and for sequence changes in PTPRD as well as the frequently deleted gene LRP1B. (kb.se)
  • This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution. (nih.gov)
  • For orthologous genes in other vertebrate species, use the same symbol as in human, rat, and mouse, whenever possible. (jax.org)
  • A potential problem in those studies is that the non-disease genes contained a large number of essential genes - genes which are indispensable for humans to survive and reproduce. (biomedcentral.com)
  • Here we perform a comparative study on the features of human essential, disease, and other genes. (biomedcentral.com)
  • In the absence of a set of well defined human essential genes, we consider a set of 1,789 ubiquitously expressed human genes (UEHGs), also known as housekeeping genes, as an approximation. (biomedcentral.com)
  • Our findings systematically confirm that disease genes have an intermediate essentiality which is less than housekeeping genes but greater than other human genes. (biomedcentral.com)
  • The human genome may contain thousands of essential genes having features which differ significantly from disease and other genes. (biomedcentral.com)
  • Identification of novel genes associated with human diseases is among the most critical tasks in medical research. (biomedcentral.com)
  • One common problem with these studies is that human essential genes were ignored and simply grouped together with other non-disease genes. (biomedcentral.com)
  • Thus, it is beneficial to separate human essential genes from other non-disease genes before comparisons are made. (biomedcentral.com)
  • Although it is almost certain that the human genome also contains hundreds to thousands of essential genes, it's impractical to experimentally determine them as in S. cerevisiae or C. elegans . (biomedcentral.com)
  • The absence of a set of well-defined human essential genes poses a challenge on studying them and urges for alternative solutions. (biomedcentral.com)
  • Based on the unique properties of the ubiquitously expressed human genes (UEHGs), we believe that they are suitable candidates for essential genes. (biomedcentral.com)
  • In this study, we consider a set of 1,789 ubiquitously expressed human genes (UEHGs) as an approximation for essential genes. (biomedcentral.com)
  • Many of these hotspot regions of CNV formation are functionally relevant, with a bias toward genes involved in immune function, some of which were previously shown to evolve under balancing selection in humans. (biomedcentral.com)
  • At least 50,000 lncRNAs are expressed from intergenic regions of the human genome, more than twice the number of protein-coding genes [ 5 ]. (biomedcentral.com)
  • The genomic organization and regulation of the murine and human resistin genes are divergent and may explain these discrepant findings ( 13 ). (diabetesjournals.org)
  • As orthologous genes are commonly mutated in canine models of human blinding disorders, canine ABCA4 appears to be an ideal candidate gene to identify and study sequence changes in dogs affected by various forms of inherited retinal degeneration. (upenn.edu)
  • This compares to more than 27,000 genes with an annotated biological process in human, and approximately 16,000 and 24,000 genes in rat and mouse respectively. (biomedcentral.com)
  • Several alternative splicing surveys have confirmed the frequent occurrence of exon skipping in human genes. (uwc.ac.za)
  • Recent improvements in mouse genome sequencing have permitted the current study to explore the occurrence of exon skipping in mouse genes orthologous to human genes on chromosome 22. (uwc.ac.za)
  • Although the transcript identity between mouse and human orthologous transcripts were high (greater than 80% sequence identity), the exon order in these gene-pairs may be different between mouse and human orthologous genes. (uwc.ac.za)
  • However, when compared to a higher estimate (52/347) of exon skipping in human genes for chromosome 22 produced under similar conditions by Hide et al.2001, it is possible that our mouse exon-skipping frequency may be lower than the human frequency. (uwc.ac.za)
  • However, the mouse exon-skipping frequency may represent the highest estimate that can be obtained given that the current number (87) of mouse genes orthologous to chromosome 22 in Ensembl (v1 30th Jan. 2002) does not deviate significantly from our total number (72) of mouse multi-exon genes. (uwc.ac.za)
  • We report that the positions of minor, U12 introns are conserved in orthologous genes from human and Arabidopsis to an even greater extent than the positions of the major, U2 introns. (biomedcentral.com)
  • Probable orthologs were identified among human and Arabidopsis genes containing U12 introns by BLAST comparison, and the intron positions were mapped onto aligned protein sequences as previously described ([ 16 ] and Additional file 1 ). (biomedcentral.com)
  • Depending on the specific variants, the zebrafish model is being investigated for the effect of perturbation of orthologous genes on retinal development. (fightforsight.org.uk)
  • With the advent of NGS technique, the explosion of NGS data generated from the tumor tissues help researchers identify driver mutations in cancer-related genes, but relatively less attention is paid to the SNP data in healthy human populations when studying cancer. (biomedcentral.com)
  • By simply dividing the human genes into cancer-related genes and other genes, we compared the features of nonsynonymous, synonymous and nonsense mutations in these two gene sets from multiple aspects. (biomedcentral.com)
  • Since its first discovery in Xenopus laevis and subsequent description in humans and mice, melanopsin genes have been described in all vertebrate classes. (ox.ac.uk)
  • Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. (cshl.edu)
  • Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. (cshl.edu)
  • The assembly of whole genomes from metagenomic sequencing reads is a very difficult problem. (biomedcentral.com)
  • Alignment of HACNS4 to orthologous sequences from nonhuman genomes. (yale.edu)
  • This need is further intensified by the human ENCODE (ENCyclopedia Of DNA Elements), mouse ENCODE, and modENCODE (model organism ENCODE) projects, to enable systematic use of the results and to further studies of functional conservation and divergence across the human, mouse, fly, and worm genomes. (biorxiv.org)
  • Four genomes - The illustration, originally part of a poster , shows syntenic relationships between human, chimpanzee, mouse and zebrafish genomes. (bcgsc.ca)
  • The scientific entry was an information graphic showing a hive panel of genomic annotations in human, mouse and dog genomes. (bcgsc.ca)
  • Sequence analysis of the Daphnia pulex genome holds some surprises that could not have been anticipated from what was learned so far from other arthropod genomes. (biomedcentral.com)
  • Simple sequence repeats (SSRs) are highly variable features of all genomes. (biomedcentral.com)
  • The classification is based on sequence similarity within the kinase domain, the presence of additional domains, known biological functions, and conservation across divergent genomes. (wormbook.org)
  • The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. (nih.gov)
  • PCR-based screening of over 500 Alu insertion loci resulted in the recovery of a few "young" Alu elements that also resided at orthologous positions in non-human primate genomes. (ojp.gov)
  • Several attempts have been made toward identification of S/MARs in genomes of various organisms including human. (researchgate.net)
  • Comparative gene mapping among human, murine, and canine genomes have the potential to rapidly identify mutations that underlie various disease syndromes. (stanford.edu)
  • One of the unique insights provided by the growing number of fully sequenced genomes is the pervasiveness of gene duplication and gene loss. (philpapers.org)
  • We analyzed the available data on U12 introns in human and Arabidopsis thaliana genomes in order to systematically compare their conservation with that of U2 introns. (biomedcentral.com)
  • The complete sequences of 50 new cDNA clones which code for large proteins. (nih.gov)
  • KEGG) database, Cluster of Orthologous Groups of proteins (COG), Gene Ontology (GO), and protein families (Pfam). (cdc.gov)
  • Only 60% of yeast and 73% of the human RBPs have functions assigned to RNA biology or structural motifs known to convey RNA binding, and many intensively studied proteins surprisingly emerge as RBPs (termed 'enigmRBPs'), including almost all glycolytic enzymes, pointing to emerging connections between gene regulation and metabolism. (nature.com)
  • The predicted structures of the Gimap proteins show common sequences and motifs, such as GTP-binding domains in the N-terminal half, but with differing C-terminal ends [ 2 , 3 ]. (hindawi.com)
  • Sequence alignment and analysis of orthologous proteins to human bactericidal/permeability-increasing protein (huBPI). (elifesciences.org)
  • A ) Sequence alignment of amino acid sequences of orthologous proteins. (elifesciences.org)
  • C ) Phylogenetic tree analysis mapping BPI orthologous proteins to their respective taxonomic ranks. (elifesciences.org)
  • A ) Sequence alignment of amino acid sequences of orthologous proteins.Functional regions I-III are framed, and positively charged amino acids are shown in blue. (elifesciences.org)
  • B ) Sequence identities of investigated orthologous proteins without signal peptide in comparison to scorpionfish BPI (scoBPI) and human BPI (huBPI). (elifesciences.org)
  • Bactericidal/permeability-increasing protein-anti-neutrophil cytoplasmic antibodies (BPI-ANCA) from people with cystic fibrosis (PwCF) do not recognize orthologous proteins of human BPI (huBPI). (elifesciences.org)
  • A complete BLASTP search of all human, and Wookiee proteins from Ensembl (Hubbard et al . (ubc.ca)
  • Toward this objective, ChIP-Seq data of 14 S/MAR binding proteins were analyzed and the binding site coordinates of these proteins were used to prepare a non-redundant S/MAR dataset of human genome. (researchgate.net)
  • For this purpose, we developed and validated an annotation method (called pairwise comparative modelling) on the basis of a three-dimensional structure (homology comparative modelling), leading to the prediction of 6,095 ARDs in a catalogue of 3.9 million proteins from the human intestinal microbiota. (nature.com)
  • We have determined the ability of 83 proteins of several families of RNA viruses (Paramyxoviridae, Flaviviridae, Orthomyxoviridae, Retroviridae and Togaviridae), to interact with 44 human autophagy-associated proteins using yeast two-hybrid and bioinformatic analysis. (sfr-biosciences.fr)
  • However, these signature sequences have not so far been extensively investigated amongst orthologous Bcl-2 family proteins. (sfr-biosciences.fr)
  • Click "Protein Details" for further information about the protein such as half-life, abundance, domains, domains shared with other proteins, protein sequence retrieval for various strains, physico-chemical properties, protein modification sites, and external identifiers for the protein. (yeastgenome.org)
  • Identification of an orthologous mammalian cytokeratin gene. (wikipedia.org)
  • First, human-specific developmental features, as elaborations on the common theme of mammalian development, are likely to arise in part from changes in the conserved genetic architecture of the developmental regulatory machinery. (yale.edu)
  • Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. (kb.se)
  • HACNSs show a statistically significant excess of human-specific sequence changes (circled) at positions highly conserved in other species. (yale.edu)
  • To this end, we have focused on identifying noncoding sequences highly conserved in nonhuman vertebrate species that display high rates of nucleotide substitution on the human lineage, which may indicate positive selection for new regulatory functions. (yale.edu)
  • In our approach, sites within CNSs were binned based on their degree of sequence conservation in six nonhuman species: chimpanzee, rhesus macaque, mouse, rat, dog and chicken, and human-specific substitutions were identified by parsimony (Fig. 1A). (yale.edu)
  • Furthermore, other near-human species such as Zeltron, Chiss , and Sullustan share the human ortholog of this locus, which supports the inference that the ancestral sequence was noncoding, and that the GLABR has de novo origins in the Wookiee. (ubc.ca)
  • These animal models may occur in non-human primates, dogs, cats, goats, mice in which mutations have been induced, or in other less common laboratory species such as bears. (stanford.edu)
  • For the phylogenetic relationships among the arboreal members of Cercopithecus , several types of molecular data, including X and Y chromosome DNA sequences, protein sequences and karyotypes, recognize a clade containing a cephus species group and a mitis group. (biomedcentral.com)
  • In this study, our objective was to perform an extensive characterization of the human gut resistome (including the capacity of ARDs to transfer between species) and to assess its dynamics under various antibiotic exposures. (nature.com)
  • C ) Sequence alignment of OAS1 p46 orthologous isoforms from different species. (bioz.com)
  • The genome sequences recently available from other primate and non-primate species showed that FOXI1 divergence patterns are compatible with neutral evolution. (biomedcentral.com)
  • However, the availability of additional FOXI orthologous sequences from a variety of species, including other primates, has permitted this initial finding to be revised. (biomedcentral.com)
  • The program netClass was then used to fill in how much of the gaps and chains contained N s (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. (nodai-genome.org)
  • Both of these branches of research examine the interrelatedness of organisms, whether within a species ( P. aeruginosa ) or between them (human vaginal microbiome). (lu.se)
  • PANTHER Pathways consists of over 165, primarily signaling, pathways, each with subfamilies and protein sequences mapped to individual pathway components. (systems-biology.org)
  • Nonsynonymous mutations change the protein sequences and are frequently subjected to natural selection. (biomedcentral.com)
  • In coding region of DNA, it is imaginable that the nonsynonymous mutations that change the protein sequences would undergo strong selection, and those nonsense mutations that cause pre-mature termination of protein synthesis are also highly deleterious and subjective to purifying selection. (biomedcentral.com)
  • These experiments have also provided evidence of functional differences between human and chimpanzee orthologs. (yale.edu)
  • To put worm kinases into an evolutionary and functional context, we compared them with the distant kinomes of human, fly, and yeast. (wormbook.org)
  • We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. (kb.se)
  • Importantly, the application allows comprehensive functional analysis through the use of orthologous relationships. (biomedcentral.com)
  • While deletion of the N-terminal extension had no significant functional impact in HeLa cells, our results suggest that the human Bcl2l10 protein evolved a calcium-binding motif in its alpha 5-alpha 6 interhelical region by acquiring critical negatively charged residues. (sfr-biosciences.fr)
  • For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. (cshl.edu)
  • The application uses various web services to gather gene sequence information, local algorithms for tandem repeats identification and similarity measures for gene clustering. (inderscience.com)
  • Most protein kinases share a common ePK (eukaryotic protein kinase) catalytic domain, and can be identified by sequence similarity with Blast or profile hidden Markov models (HMMs). (wormbook.org)
  • The remaining atypical protein kinases (aPK) belong to several families, some of which have structural, but not sequence similarity to ePKs. (wormbook.org)
  • On the basis of sequence similarity, chromosomal localisation, and phylogeny, we identify our new melanopsins as the true orthologs of the melanopsin gene previously described in mammals and term this grouping Opn4m. (ox.ac.uk)
  • Here we report the results of a collaborative study to discover somatic mutations in 188 human lung adenocarcinomas. (kb.se)
  • METHODS Here, for a mutant P. chabaudi malaria parasite and its immediate progenitor, the in vivo artemisinin resistance phenotypes and the mutations arising using Illumina whole-genome re-sequencing were compared. (gla.ac.uk)
  • Over 200 mutations in the retina specific member of the ATP-binding cassette transporter superfamily (ABCA4) have been associated with a diverse group of human retinal diseases. (upenn.edu)
  • Different mutations in the human FOXI1 gene and its regulatory binding site on SLC26A4 (also known as pendrin) have been shown to compromise the transcription of this anion transporter gene in patients with Pendred Syndrome and nonsyndromic enlargement of the vestibular aqueduct [ 2 ]. (biomedcentral.com)
  • Overall, these findings have led to the hypothesis that mutations in the human FOXI1 gene might cause sensorineural deafness with distal renal tubular acidosis and male infertility [ 4 ]. (biomedcentral.com)
  • The same goes for nonsense mutations that introduce pre-mature stop codons into CDSs (coding sequences). (biomedcentral.com)
  • The study has fully discussed the effect of synonymous mutations on splicing events, and proposed some awesome ideas like the mutations silent to the protein sequence are not always silent to the function [ 6 ]. (biomedcentral.com)
  • Main factors contributing towards the low detection of mouse exon-skipping events include the lack of mouse transcripts matching to mouse genomic sequences and the under-prediction of mouse exons. (uwc.ac.za)
  • The U12 introns were mapped onto the genomic sequences yielding 570 human and 182 Arabidopsis U12 validated intron positions available for comparative analysis (Additional file 1 ). (biomedcentral.com)
  • This thematic series of companion papers constitutes the initial exploration of the genome biology of the waterflea (Daphnia) building on the first complete crustacean genome sequence. (biomedcentral.com)
  • We report here the genome sequence of the Brown Norway (BN) rat strain. (nih.gov)
  • The S. cerevisiae Reference Genome sequence is derived from laboratory strain S288C . (yeastgenome.org)
  • We present here a draft genome sequence of the red jungle fowl, Gallus gallus. (cshl.edu)
  • Modification of the multiplex plasmid PCR assay for Borrelia miyamotoi strain LB-2001 based on the complete genome sequence reflecting genomic rearrangements differing from strain CT13-2396. (cdc.gov)
  • The primer pair sets specific for each plasmid were derived from the genome sequence for B. miyamotoi strain CT13-2396, because the LB-2001 complete sequence had not been generated. (cdc.gov)
  • The recent completion of the LB-2001 genome sequence revealed a distinct number of plasmids (n=12) that differed from CT13-2396 (n=14). (cdc.gov)
  • The information in this database is authored by biological researchers with expertise in their fields, maintained by the Reactome editorial staff, and cross-referenced with the sequence databases at NCBI , Ensembl and UniProt, the UCSC Genome Browser , HapMap, KEGG ( Gene and Compound), ChEBI , PubMed and GO . (systems-biology.org)
  • Comparison of our mouse exon-skipping events to previously detected human exon-skipping events on chromosome 22 by Hide et al.2001, has revealed that mouse and human exon-skipping events were never observed together within an orthologous gene-pair. (uwc.ac.za)
  • Circular genome maps were generated using Circos (Version 0.64) based on analysis of the coverage of sample sequencing reads, single-nucleotide polymorphisms (SNPs), and InDels. (cdc.gov)
  • At the genic level, single nucleotide polymorphisms (SNPs) in noncoding regions of the human resistin gene were either not significantly associated with insulin resistance ( 4 , 5 ) or associated with an insulin sensitivity index in the case of a different promoter SNP from the one that we present in this article ( 6 ). (diabetesjournals.org)
  • Canine ortholog cDNA sequence was cloned and verified using RPE/choroid 5′- and 3′-RACE. (upenn.edu)
  • The gene sequences were downloaded from the NCBI. (cdc.gov)
  • We have constructed a second-generation, high-resolution CNV map for the rhesus macaque and combined it with similar CNV data for the chimpanzee and ultra-high-resolution CNV data from humans to determine comprehensively the location and structure of primate CNV hotspots. (biomedcentral.com)
  • In order to identify primate hotspots for CNV formation, we compiled CNV datasets for human, chimpanzee and rhesus macaque. (biomedcentral.com)
  • Our sequence analysis of the complete canine ABCA4 coding region will clearly provide a baseline and tools for future association studies and comparative genomics to further delineate the role of ABCA4 in canine blinding disorders. (upenn.edu)
  • We failed to identify any copy number differences within the SHFM3 orthologous genomic locus between Dac mutant and wild-type littermates, showing that the Dactylaplasia alleles are not associated with duplications of the region, in contrast with the described human SHFM3 cases. (unige.ch)
  • Click "Sequence Details" to view all sequence information for this locus, including that for other strains. (yeastgenome.org)
  • Sequencing of amplicons from the expression locus of the reisolates confirmed the presence of a predominant majority serotype population with minority variants. (cdc.gov)
  • Scattered repeat sequences were predicted by RepeatMasker software, and TRF searched for tandem repeats in DNA sequences. (cdc.gov)
  • Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function. (kb.se)
  • My research focused on the identification and characterization of animal models of human diseases. (stanford.edu)
  • In natural infections of the human malaria parasite P. falciparum, 12 polymorphisms (nine SNPs and three indels) were identified in the orthologous gene. (gla.ac.uk)
  • Here, we analyzed the publically available human SNPs. (biomedcentral.com)
  • Protein-alignment-guided assembly of orthologous gene families complements whole-metagenome assembly in a new and very useful way. (biomedcentral.com)
  • The location of each human-specific substitution is indicated by a red box above the alignment. (yale.edu)
  • Sequence alignment and analysis of orthologous Actinopterygii bactericidal/permeability-increasing protein (BPI). (elifesciences.org)
  • A ) Sequence alignment of human OAS1 isoforms. (bioz.com)
  • and datamining publicly available metagenomic datasets from the human vaginal tract, to identify protein-coding gene clusters in the bacteria that make up the majority of the microbiome of the vagina. (lu.se)
  • Interestingly, the Dac2j mutation occurs within a highly conserved element that may represent a regulatory sequence for a neighboring gene. (unige.ch)
  • The capture of mouse exon-skipping events may increase as the quality and quantity of mouse genomic and transcript sequences improves. (uwc.ac.za)
  • Article: An integrative approach for codon repeats evolutionary analyses Journal: International Journal of Data Mining and Bioinformatics (IJDMB) 2012 Vol.6 No.4 pp.369 - 381 Abstract: The relationship between genome characteristics and several human diseases has been a central research goal in genomics. (inderscience.com)
  • The second, more practical consideration is that evolutionary conservation provides a means to interpret the statistical and ultimately biological importance of human-specific sequence changes. (yale.edu)
  • In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. (cshl.edu)
  • Identification of "human accelerated" conserved noncoding sequences (HACNSs). (yale.edu)
  • The systematic identification of conserved developmental regulatory elements has made it possible to study the impact of human-specific changes in regulatory DNAs on a genome-wide scale. (yale.edu)
  • ESTs and BAC/YAC ends: use the assigned sequence accession identification numbers. (jax.org)
  • The study was a large team effort involving researchers in the UK, from the Babraham Institute, the University of Manchester, the Sanger Institute and the University of Cambridge, in Australia, from the University of Melbourne, and the USA, from the University of Texas at San Antonio (all part of the Sequence Analysis of Vertebrate Orthologous Imprinted Regions 'SAVOIR' consortium). (eurekalert.org)
  • Anticipated orthologous ORFs in the regions above were defined as BLAT (Kent 2002) or SSearch (Pearson and Lipman 1988) sequence matches. (ubc.ca)
  • It is useful for finding orthologous regions and for studying genome rearrangement. (nodai-genome.org)
  • The differences between the nature of the human and mouse genomic abnormalities argue against models proposed so far that either envisioned SHFM3 as a local trisomy or Dac as a mutant allele of Fbxw4. (unige.ch)
  • We are using in vivo mouse transgenic assays to examine particular HACNSs from our current dataset for human-specific gene regulatory functions by comparison to chimpanzee and rhesus orthologs (Fig. 3). (yale.edu)
  • In this study, we identified over 2,000 human CNVs that overlap with orthologous chimpanzee or orthologous macaque CNVs. (biomedcentral.com)
  • Such candidates are then being further analysed using human and macaque retina RNA data, as well as RNA data from iPSC derived patient cells. (fightforsight.org.uk)
  • We present evidence for the de novo origin of the Wookiee wookiee protein-coding gene GLABR since their divergence from humans. (ubc.ca)
  • In this paper, we have unraveled two major sites of divergence between human Bcl2l10 and its vertebrate homologs. (sfr-biosciences.fr)
  • Pask explains that the microRNA structure is virtually identical to that of mice and humans, but there was no evidence of this gene or a similar microRNA in the more distantly related platypus. (eurekalert.org)
  • Human-specific substitutions at sites conserved from chimpanzee to chicken are expected to be uncommon events, and were consequently given more weight than substitutions at less conserved sites. (yale.edu)
  • We are dissecting a number of elements in detail using a synthetic approach, in which subsets of the human-specific sequence changes in each element are transferred into the chimpanzee enhancer sequence. (yale.edu)
  • To assess how well gene sequences are detected for different organisms, we report the number of organisms for which the longest mapped contig covers at least half of the corresponding reference sequence. (biomedcentral.com)
  • 6 families appear to have been lost from nematodes, based on their presence in fly, human and more basal organisms ( Table 1 ), and several new families have been invented within the coelomate lineage, whose functions predominantly map to immunity/angiogenesis, neurobiology, cell cycle and morphogenesis. (wormbook.org)
  • ous organisms including human. (researchgate.net)
  • Microbiome sequencing projects typically collect tens of millions of short reads per sample. (biomedcentral.com)
  • Many studies have shown that specific gene patterns, such as amino acid repetitions, are associated with human diseases. (inderscience.com)
  • The relationship between genome characteristics and several human diseases has been a central research goal in genomics. (inderscience.com)
  • Because there is no back up copy, when errors occur in this process, it results in many human genetic diseases mainly affecting growth and brain function. (eurekalert.org)
  • Understanding how genetic imprinting evolved is important," said Dr Shaw, "It helps us to determine how the mechanism works and what we can do to avoid the development of a number of human diseases. (eurekalert.org)
  • Animal models offer a unique opportunity to study the pathogenesis of neurologic diseases afflicting both humans and animals. (stanford.edu)
  • Inherited diseases in dogs reliably replicate many hereditary diseases in humans. (stanford.edu)
  • Fungi are ubiquitous airborne allergens and are important causes of human diseases, especially in the upper and lower respiratory tracts. (medscape.com)
  • DNA methylation, particularly 5-methylcytosine (5mC) at CpG sequences, is widely conserved in eukaryotes. (elifesciences.org)
  • Depending on the goals of the project, the short reads can either be subjected to direct sequence analysis or be assembled into longer contigs. (biomedcentral.com)
  • Sequence analysis showed that these "young" Alu insertions represented gene conversion events of pre-existing ancient Alu elements or independent parallel insertions of older Alu elements in the same genomic region. (ojp.gov)
  • This means that I have a role in the research from when we receive tissue biopsies from women with PCOS, sequencing it and performing the data analysis and drawing biological conclusions. (lu.se)
  • The human sequence used in this annotation is from the Mar. 2006 (hg18) assembly. (nodai-genome.org)
  • To explore the scope of RBPs across eukaryotic evolution, we determined the in vivo RBP repertoire of the yeast Saccharomyces cerevisiae and identified 678 RBPs from yeast and additionally 729 RBPs from human hepatocytic HuH-7 cells. (nature.com)
  • Additionally, we explored for signals of natural selection within humans by sequencing the gene in 20 Europeans, 20 East Asians and 20 Yorubas and by analysing SNP variation in a 2 Mb region centered on FOXI1 in 39 worldwide human populations from the HGDP-CEPH diversity panel. (biomedcentral.com)
  • may be especially important in our own evolution since it appears that the "revolving door" of gene duplication and loss has undergone multiple accelerations in the lineage leading to humans. (philpapers.org)
  • Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. (kb.se)
  • Enables DNA-binding transcription activator activity, RNA polymerase II-specific and sequence-specific DNA binding activity. (nih.gov)
  • Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. (zfin.org)
  • Orthologous to human KLF13 (KLF transcription factor 13). (zfin.org)
  • The human FOXI1 gene codes for a transcription factor involved in the physiology of the inner ear, testis, and kidney. (biomedcentral.com)
  • We further show that both Dac1j and Dac2j are caused by insertions of MusD retroelements that share 98% sequence identity. (unige.ch)
  • To identify putative regulatory sequences evolving rapidly on the human lineage, we developed a test statistic (in collaboration with Shyam Prabhakar of the Genome Institute of Singapore) for assessing the significance of human-specific sequence acceleration in conserved noncoding sequences (CNSs). (yale.edu)
  • These loci may have been hotspots of cis-regulatory change throughout human evolution. (yale.edu)
  • Therefore, we aimed to examine whether the autoregulation-integrated FFC is a network motif relevant to describing the human transcriptional regulatory systems, and explored the relationship of such network motifs with biological functions. (biomedcentral.com)
  • For this purpose, we examined the influence of integrating autoregulation into the FFC on the number of FFC appearances by surveying the human transcriptional regulatory network. (biomedcentral.com)
  • For example, non-human primates develop many of the same cognitive deficits and neuropathologic changes as occur in humans. (stanford.edu)
  • Nematodes share 153 subfamilies with human, providing close homologs for 81% (419/518) of all human kinases. (wormbook.org)
  • Until now, all of these sequences have been considered representatives of a single orthologous gene (albeit with duplications in the teleost fish). (ox.ac.uk)
  • Research published in Nature Genetics by a team of international scientists including the department of zoology at the University of Melbourne, Australia, has established an identical mechanism of genetic imprinting, a process involved in marsupial and human fetal development, which evolved 150 million years ago. (eurekalert.org)
  • This paper shows that we share a common genetic imprinting mechanism which has been active for about 150 million years despite the differences in reproductive strategies between marsupials and humans," said Professor Geoffrey Shaw of the Department of Zoology at the University of Melbourne, a coauthor on the paper. (eurekalert.org)
  • In addition, the study identified the human genetic variation associated with the L1 insertion polymorphisms in major geographic groups. (ojp.gov)
  • Professor Marilyn Renfree who lead the University of Melbourne research team says marsupials give birth to very small young that develop mainly within the pouch while humans have more developed young at birth that undergo a large period of growth in the uterus. (eurekalert.org)
  • The human genome has an extremely complex tissue expression profile. (biomedcentral.com)
  • Resistin expression in humans has been reported at low levels in the adipose tissue of some but not all humans ( 7 , 8 ), and its reduced expression has also been proposed as a hallmark of obesity ( 9 ). (diabetesjournals.org)
  • Concerted evolution refers to the pattern in which copies of multigene families show high intraspecific sequence homogeneity but high interspecific sequence diversity. (biomedcentral.com)
  • Kinases are deeply conserved in evolution, and the worm has family homologs for over 80% of the human kinome. (wormbook.org)
  • This partitioning strategy facilitated a formal test of the likelihood of observing the exact configuration of human-specific substitutions in a CNS, compared with what would be expected in a typical CNS showing a comparable level of conservation and located in region of the genome of comparable background neutral rate. (yale.edu)