• a , Maximum-likelihood tree using concatenated protein sequences of 100 genes randomly selected from 4,694 Fusarium orthologous genes that have clear 1:1:1:1 correlation among the Fusarium genomes and have unique matches in Magnaporthe grisea , Neurospora crassa and Aspergillus nidulans . (nature.com)
  • Cloning and sequencing of the phn (psiD) genes involved in alkylphosphonate uptake and C-P lyase activity in Escherichia coli B. (embl-heidelberg.de)
  • have analyzed the tef-1α sequences of F. equiseti , as well as the toxin-related genes PKS13 , PKS4, and TRI5 [26], and Kari has successfully cloned a protease gene [27]. (researchsquare.com)
  • 10,200 protein-encoding genes were predicted based on the genome sequence. (springeropen.com)
  • The genes and proteins were predicted and annotated based on the genome sequence. (springeropen.com)
  • Many retroposed sequences have maintained ORFs, suggesting a functional role for these genes. (biomedcentral.com)
  • Homology candidate relations are integrated into a global network and groups of homologous genes are extracted by applying a community detection algorithm. (biomedcentral.com)
  • Homologous genes can be distinguished into paralogous, when homology occurs within the same genome, or orthologous, when homology occurs between different genomes. (biomedcentral.com)
  • Core genes are often under strong evolutionary selection, thus their sequences are transmitted almost without any alteration. (biomedcentral.com)
  • The amount of variations affecting dispensable genes varies and the similarity between homologous sequences tends to decrease according to their phylogenetic distance. (biomedcentral.com)
  • The env genes contain a cis-acting RNA target sequence for the rev protein (= GENE PRODUCTS, REV ), termed the rev-responsive element (RRE). (lookformedical.com)
  • When making a judgment in cases of small genes, or genes comprised of small exons, available evidence was classified as three types: (1) Matches to cDNA sequence data, which could be the BDGP cDNA/EST data or data generated by the community, and such data was considered more significant if it included an intron with consensus splice sites. (fruitfly.org)
  • We sequenced the worm's ~ 688-Mb haploid genome with an overall completeness of ~ 95% and discovered that L. luymesi lacks many genes essential in amino acid biosynthesis, obligating them to products provided by symbionts. (biomedcentral.com)
  • To further understand the mechanism of the developmental switch from fronds to turions, we cloned and sequenced the genes of three large-subunit ADP-glucose pyrophosphorylases ( APLs ). (biomedcentral.com)
  • Scoring the Alignment of Amino Acid Sequences Constructing PAM and Blosum Matrices. (progsound.de)
  • A 'profile' (defined as a consensus primary structure model consisting of position-specific residue scores and insertion or deletion penalties) is an intuitive step beyond the pairwise sequence alignment methods. (biopred.net)
  • PanDelos avoids sequence alignment by introducing a measure based on k -mer multiplicity. (biomedcentral.com)
  • Dayhoff compiled one of the first protein sequence databases, initially published as books and pioneered methods of sequence alignment and molecular evolution. (ind.in)
  • The avenins of oats have lower sequence similarity and a low toxicity profile. (karger.com)
  • Ectopic recombination is typically mediated by sequence similarity at the duplicate breakpoints, which form direct repeats. (ipfs.io)
  • Replication slippage is also often facilitated by repetitive sequences, but requires only a few bases of similarity. (ipfs.io)
  • A challenge on this field is that of designing fast and adaptive similarity measures in order to find a suitable pan-genome structure of homology relations. (biomedcentral.com)
  • When closely related organisms are analyzed, reasonable thresholds on sequences similarity are applied to recognize gene families. (biomedcentral.com)
  • The phylogenetic diversity of a population of 84 Beauveria strains -mainly B. bassiana (n = 76) - isolated from temperate, sub-tropical and tropical habitats was examined by analyzing the nucleotide sequences of two mt intergenic regions ( atp 6- rns and nad 3- atp 9) and the nuclear ITS1-5.8S-ITS2 domain. (biomedcentral.com)
  • Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. (lookformedical.com)
  • The specificity of the proteins is determined by the sequences outside the repeats themselves. (embl.de)
  • We chose proteins that include amino and carboxyl extensions as well as proteins that are made up entirely of WD-repeats. (embl.de)
  • Formins are multidomain proteins defined by a conserved FH2 (formin homology 2) domain with actin nucleation activity preceded by a proline-rich FH1 (formin homology 1) domain. (biomedcentral.com)
  • Previously, the genome of the cereal pathogen Fg was sequenced and shown to encode a larger number of proteins in pathogenicity related protein families compared to non-pathogenic fungi, including predicted transcription factors, hydrolytic enzymes, and transmembrane transporters 5 . (nature.com)
  • Sequence homology searches identify PhnC, PhnK, PhnL, and, possibly, PhnN proteins as members of nucleotide-binding proteins of the binding protein-dependent transport systems. (embl-heidelberg.de)
  • BLOSUM62 is the matrix calculated by using the observed substitutions between proteins which have at most 62 sequence identity, etc. replacements are counted on the branches of a phylogenetic. (progsound.de)
  • Computational analysis is increasingly important for inferring the functions and structures of proteins [1] because the speed of DNA sequencing has long since surpassed the rate at which the biological function of sequences can be elucidated experimentally. (biopred.net)
  • Established sequence comparison algorithms detect significant similarities between known database sequences and 35-80% of new proteins, depending on the organism. (biopred.net)
  • An increase of a single percentage point may mean learning something useful about an additional 700 human proteins by the time elucidation of the sequence of the human genome nears completion round about the year 2002. (biopred.net)
  • However, most proteomic studies rely on consensus databases to match spectra to peptide and proteins sequences, and thus remain limited to the analysis of canonical protein sequences. (biorxiv.org)
  • Most commonly, this approach leverages high-resolution mass spectrometric measurements of proteolyzed proteins, combined with tandem peptide fragmentation to match observed spectra with those expected from their amino acid composition. (biorxiv.org)
  • 11 And human diseases, including cancer in particular, tend to be defined by the presence of proteins with altered and pathogenic sequences. (biorxiv.org)
  • DNA sequences that form the coding region for the viral envelope (env) proteins in retroviruses. (lookformedical.com)
  • WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide. (embl.de)
  • These larger cathelicidins display repetitive proline motifs forming extended polyproline-type structures. (wikipedia.org)
  • Les isolats furent class s en deux groupes bas s sur le nombre de motifs r p t s 2 par 2 (tandem repeats) compos s de 6 paires de bases au sein du g ne rpoT. (ilsl.br)
  • citation needed] Cathelicidins range in size from 12 to 80 amino acid residues and have a wide range of structures. (wikipedia.org)
  • Most cathelicidins are linear peptides with 23-37 amino acid residues, and fold into amphipathic α-helices. (wikipedia.org)
  • Even larger cathelicidin peptides (39-80 amino acid residues) are also present. (wikipedia.org)
  • The cathelicidin family shares primary sequence homology with the cystatin family of cysteine proteinase inhibitors, although amino acid residues thought to be important in such protease inhibition are usually lacking. (wikipedia.org)
  • Suppose I start with a given polypeptide sequence M at time t, and observe the evolutionary changes in the sequence until 1 of all amino acid residues have undergone substitutions at time tn. (progsound.de)
  • Multiple alignments of protein sequence families indicate residues that are more conserved than others, and the points at which insertions and deletions are more frequent. (biopred.net)
  • We sequenced Fv strain 7600 and Fol strain 4287 (Methods, Supplementary Table 1 ) using a whole-genome shotgun approach and assembled the sequence using Arachne ( Table 1 , ref. 6 ). (nature.com)
  • In this study, the Illumina HiSeq 4000 and PacBio platforms were used to sequence and assemble the whole genome of Fusarium equiseti D25-1. (researchsquare.com)
  • Advances in whole-genome sequencing technologies have enabled numerous key discoveries. (researchsquare.com)
  • As whole genome sequences became available, again with the pioneering work of Frederick Sanger, the term bioinformatics was re-discovered to refer to the creation of databases such as GenBank in 1982. (ind.in)
  • 18. What nucleic acid does in situ hybridization stain? (examyear.com)
  • 3, 137-155 (1996) REFERENCE 9 AUTHORS Fujita,N., Mori,H., Yura,T. and Ishihama,A. TITLE Systematic sequencing of the Escherichia coli genome: analysis of the 2.4-4.1 min (110,917-193,643 bp) region JOURNAL Nucleic Acids Res. (nig.ac.jp)
  • Recent advances in nucleic acid sequencing now permit rapid and genome-scale analysis of genetic variation and transcription, enabling population-scale studies of human biology, disease, and diverse organisms. (biorxiv.org)
  • With the public availability of data tools for their analysis were quickly developed and described in journals such as Nucleic Acids Research which published specialized issues on bioinformatics tools as early as 1982. (ind.in)
  • Transposable elements (TEs) are ancient (retro)-virus insertions inside a host genome and are peculiar mobile genetic elements accounting for a large proportion of repetitive DNA regions ( [29] ). (sisef.it)
  • One is faced with a number of difficult problems: what are the best ways to set the position-specific residue scores, to score gaps and insertions, and to combine structural and multiple sequence information? (biopred.net)
  • PG2 integrates genome and transcriptome sequencing to incorporate protein variants containing amino acid substitutions, insertions, and deletions, as well as non-canonical reading frames, exons, and other variants caused by genomic and transcriptomic variation. (biorxiv.org)
  • Duplications arise from an event termed unequal crossing-over that occurs during meiosis between misaligned homologous chromosomes.The chance of this happening is a function of the degree of sharing of repetitive elements between two chromosomes. (ipfs.io)
  • Following duplication events, the resulting stretches of homologous sequence can promote recombination between gene copies. (elifesciences.org)
  • Distinguishing three-dimensional structures characteristically formed by homologous protein sequences. (bvsalud.org)
  • When digestive enzymes are insufficient to break gliadorphin down into 2-3 amino acid lengths and a compromised intestinal wall allows for the leakage of the entire 7 amino acid long fragment into the blood, glaidorphin can pass through to the brain through circumventricular organs and activate opioid receptors resulting in disrupted brain function. (greenmedinfo.com)
  • There is a block consisting of 11 direct and 7 inverted repeats outside the open reading frame, the sequence ATACTAATGGCGCACC being the base of the repeats. (cytgen.com)
  • Mt sequences allowed better differentiation of strains than the ITS region. (biomedcentral.com)
  • In addition, we sequenced 99 ospC flanking sequences from different lineages and compared the complete cp26 sequences of 11 strains as well as the cp26 bbb02 loci of 56 samples. (cdc.gov)
  • Pairwise sequence comparison methods such as BLAST and FASTA generally assume that all amino acid positions are equally important even though a great deal of position-specific information is usually available for a protein or protein family of interest. (biopred.net)
  • We sequenced two additional Fusarium species, Fv , a maize pathogen that produces fumonisin mycotoxins that can contaminate grain, and F. oxysporum f.sp. (nature.com)
  • In this study, the complete genomic sequence of Fusarium equiseti D25-1 was determined using multiple sequencing platforms. (researchsquare.com)
  • The cloning and sequencing of amplification products and a Cleaved Amplified Polymorphisms (CAPs) approach on the identified retrotransposons, showed a high level of diversity among the multiple copies of both elements. (sisef.it)
  • Similarities in amino acid sequences between various organisms also suggest common descent, and the fossil record also shows cases in which one plant or animal type evolved into different types over time. (rationalwiki.org)
  • The I1-type amplicon resistance plasmids prompted us to develop a polymerase sequences were identical to the R64 IncI1 reference plas- chain reaction (PCR)-based replicon typing method ( 4 ). (cdc.gov)
  • Polymerase chain reaction (PCR) followed by DNA sequencing was performed targeting the rpoT gene of M. leprae . (ilsl.br)
  • La r action de polymerase en chain (PCR) suivie par le s quen age des produits obtenus fut r alis e sur le g ne rpoT de M. leprae . (ilsl.br)
  • The paper presents the results of analysis of the primary sequence of repetitive barley DNA called BRS1 (index number in Genbank BRS-1 U72261). (cytgen.com)
  • The exception is the final exon which not only codes the terminal portion of the receptor, but also includes a 2,147 bp non-coding sequence that follows. (creation.com)
  • All three putative protein and exon sequences were conserved, but the corresponding genomic sequences were extremely variable mainly due to the invasion of miniature inverted-repeat transposable elements (MITEs) into introns. (biomedcentral.com)
  • However, recent studies in many organisms and in humans have revealed significant protein sequence variation due to the presence of somatically acquired genetic variants, alternative transcription, and mRNA splicing, which are not necessarily annotated in reference databases. (biorxiv.org)
  • Anatomical homologies - Throughout the domains of life, organisms show a distinct pattern of constraints based on homology in the development and construction of the body. (rationalwiki.org)
  • Regardless of the slight differences, all organisms use the same coding mechanism for translating the code into amino acid sequences. (rationalwiki.org)
  • Single-cell RNA-sequencing analysis demonstrated the accelerated differentiation within CD8 compartments, enhanced cytotoxic pathways in CD8 TEMRA and TEM cells, while CD8 central memory (TCM) and naïve cells were already more-active and transcriptionally-reprogrammed. (bvsalud.org)
  • To begin a characterization of the transition from the growth to the dormant phase we used abscisic acid (ABA), a plant hormone, to induce controlled turion formation in Spirodela polyrhiza and investigated their differentiation from fronds, representing their growth phase, into turions with respect to morphological, ultra-structural characteristics, and starch content. (biomedcentral.com)
  • We gathered a series of 49 individuals from 33 families with RAD21 alterations [24 different intragenic sequence variants (2 recurrent), 7 unique microdeletions], including 24 hitherto unpublished cases. (springer.com)
  • Data that typically supported a new gene annotation included BDGP EST and cDNA data, GenBank/EMBL/DDBJ submissions from the scientific community, convincing BLASTX homologies, community submissions of sequence data to FlyBase, or reassessment of gene prediction data. (fruitfly.org)
  • Profiles' of protein structures and sequence alignments can detect subtle homologies. (biopred.net)
  • Replication slippage is an error in DNA replication that can produce duplications of short genetic sequences. (ipfs.io)
  • ALT, however, promotes telomere elongation using homology directed DNA damage repair via break induced replication [ 1 - 4 ]. (oncotarget.com)
  • ALT was recently described to resemble break-induced replication (BIR), a specific homology directed repair pathway utilized to repair one-sided DNA double-stranded breaks that are often generated following replication fork collapse [ 4 ]. (oncotarget.com)
  • Pan-genome approaches afford the discovery of homology relations in a set of genomes, by determining how some gene families are distributed among a given set of genomes. (biomedcentral.com)
  • Sequences shared by a subset of genomes are referred as dispensable and they represent variable features. (biomedcentral.com)
  • We present a detailed sequence analysis of the 10 formins (ForA to J) identified in the genome of the social amoeba Dictyostelium discoideum . (biomedcentral.com)
  • A detailed secondary metabolism analysis and structure verification of the main ingredients were performed, and the biosynthesis pathways of seven ingredients (mannitol, cordycepin, purine nucleotides, pyrimidine nucleotides, unsaturated fatty acid, cordyceps polysaccharide and sphingolipid) were predicted and drawn. (springeropen.com)
  • During the past year, applications of these powerful new HMM-based profiles have begun to appear in the fields of protein-structure prediction and large-scale genome-sequence analysis. (biopred.net)
  • In this review, I will explain what HMMs are, describe their strengths and limitations, and highlight how HMM-based profiles are beginning to be used in protein structure prediction and large-scale genome sequence analysis. (biopred.net)
  • PG2 can be integrated with current and emerging sequencing technologies, assemblers, variant callers, and mass spectral analysis algorithms, and is available open-source from https://github.com/kentsisresearchgroup/ProteomeGenerator2 . (biorxiv.org)
  • Another early contributor to bioinformatics was Elvin A. Kabat , who pioneered biological sequence analysis in 1970 with his comprehensive volumes of antibody sequences released with Tai Te Wu between 1980 and 1991. (ind.in)
  • This study reveals a new mechanism for the fluid gain of beneficial mutations in genetic regions undergoing active recombination in viruses and illustrates the value of long read sequencing technologies for investigating complex genome dynamics in diverse biological systems. (elifesciences.org)
  • Sep 4, 2018 PAM vs BLOSUM score matrices 5 minute read Amino acids, nucleotides or any other evolutionary character are replaced by others at some rate. (progsound.de)
  • In order to clarify the biological and pharmacological mechanisms of O. sinensis , we carried out the genome sequencing of H. sinensis, anamorph of O. sinensis , for the first time, described the annotation and gene expression, and analyzed the complete sequencing data (Li et al. (springeropen.com)
  • Gene splits or merges were a common annotation correction and were based upon EST/cDNA data, BLASTX homologies, or corrections submitted by the community. (fruitfly.org)
  • Repetitive genetic elements such as transposable elements offer one source of repetitive DNA that can facilitate recombination, and they are often found at duplication breakpoints in plants and mammals. (ipfs.io)
  • ALT is a recombination-based mechanism where one telomere uses other chromosomal, or extrachromosomal, telomeric DNA sequences as a template for telomere elongation. (oncotarget.com)
  • By means of DNA sequencing of a large sample collection of the pathogen from across the United States, we studied the gene for the bacterium's highly diverse OspC protein, protective immunity against which develops in animals. (cdc.gov)
  • Within the HMM formalism, it is possible to apply formal, fully probabilistic methods to profiles and gapped sequence alignments. (biopred.net)
  • The complete nucleotide sequence of 15,611 bases has been determined, and the gene structures were examined. (embl-heidelberg.de)
  • Based mostly on our crystal structures and homology modeling, we recognized five amino acids surrounding the inhibitor binding site that we hypothe sized could contribute to inhibitor selectivity. (phosphorylase-signal.com)
  • United States Patent 8,932,814 CRISPR-Cas nickase systems, methods and compositions for sequence manipulation in eukaryotes. (stanford.edu)
  • X73674), which caused 3 amino acid variations. (cdc.gov)
  • The nucleotide and deduced amino acid sequences of the phnA gene showed no significant homology with any data bank accessions. (embl-heidelberg.de)
  • For gene models with only one of these three types of supporting data, models with a predicted CDS greater than 100 amino acids were created or retained. (fruitfly.org)
  • In cases for which two or more types of supporting data existed, a gene model was created if the predicted CDS exceeded 50 amino acids. (fruitfly.org)
  • BLOSUM 62 is a matrix calculated from comparisons of sequences with a pairwise identity of no more than 62. (progsound.de)
  • The BLOSUM and PAM matrices are square symmetric matrices with integer coefficients, whose row and column names are identical and unique each name is a single letter representing a nucleotide or an amino acid. (progsound.de)
  • The central, catalytic domain of GRKs is actually a serine threonine kinase domain 32% identical in sequence to your catalytic subunit of protein kinase A and is thus a member in the PKA, PKG, and PKC family members of kinases. (phosphorylase-signal.com)
  • Using enhanced long-read single-cell isoform sequencing, we comprehensively analyze RNA isoforms in multiple mouse brain regions, cell subtypes, and developmental timepoints from postnatal day 14 (P14) to adult (P56). (biorxiv.org)
  • Comparing multiple sequences manually turned out to be impractical. (ind.in)
  • The non-WD-repeat amino terminal alpha helix of G beta does not inhibit folding because G beta does not fold even when this region is removed. (embl.de)
  • Two retrotransposons, belonging to the two major classes of LTR and non-LTR elements, were characterized trough a SCAR (Sequence Characterized Amplified Region) strategy. (sisef.it)
  • Fourteen repetitive extragenic palindromic sequences are found in the phn DNA: 10 exist in the extragenic region between phnA and phnB, two between phnD and phnE, and two between phnK and phnL. (embl-heidelberg.de)
  • 99% sequence identity in the coding region and obtained evidence for the expression of an alternative Gpi1 transcript in mouse spermatogenic cells. (biomedcentral.com)
  • DNA sequences that form the coding region for retroviral enzymes including reverse transcriptase, protease, and endonuclease/integrase. (lookformedical.com)
  • El an lisis se hizo por la reacci n en cadena de la polimerasa (PCR) y por secuenciaci n del DNA de la region correspondiente al gene rpo T de M. leprae . (ilsl.br)
  • Gliadorphin is a 7 amino acid long peptide: Tyr-Pro-Gln-Pro-Gln-Pro-Phe which forms when the gastrointestinal system is compromised. (greenmedinfo.com)
  • Using long sequencing reads from the Oxford Nanopore Technologies platform, we phased SNVs within large gene copy arrays for the first time. (elifesciences.org)
  • Los aislados se clasificaron en dos grupos con base en el n mero de 'secuencias tandem' compuestas por 6 pares de bases en el gene rpo T. Los aislados de Jap n (excepto Okinawa) y Korea correspondieron a un genotipo, mientras que los aislados de los pa ses del sudeste asi tico, Brazil, Haiti, y Okinawa en Japon, correspondieron a un segundo genotipo. (ilsl.br)