Similarity or repetitive sequences. Medical search. Frequent questions

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)
A second critical goal was to map and sequence the genomes of several important model organisms: specifically, the bacterium E. coli, yeast, the roundworm, fruit fly, and mouse. (probe.org)
Since many sequencing technologies produce reads that are significantly shorter than the target genome size, a process to construct contigs, scaffolds, and full-length genomes is needed. (biomedcentral.com)
Yet there is a more insidious reason, Meissner explains: "Most genomes - including those of humans and mice - contain thousands of virus-derived sequences that have embedded themselves in the genomes of their hosts over the last few million years. (bionity.com)
Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. (biomedcentral.com)
From the beginning, the project has also played a large part in driving the development of technology that aided the high-throughput sequencing of genomes from other model organisms such as mouse, worm and yeast. (ubc.ca)
1 This realization begged the question, Why would these disparate organisms-humans and mice-have very similar sequences placed in the same locations in their respective genomes? (reasons.org)
Using the Yellow Line, you can prospect entire genomes for similarity to specific sequences. (cshl.edu)
Use the Yellow Line to search a number of genomes with the DNA or protein sequence as query. (cshl.edu)
The high degree of similarity between the mouse and human genomes is demonstrated through analysis of the sequence of mouse chromosome 16 (Mmu 16), which was obtained as part of a whole-genome shotgun assembly of the mouse genome. (inrae.fr)

Although a high degree of similarity exists between the two sequenced Pseudomonads, 976 protein-encoding genes are unique to Pss B728a when compared with Pst DC3000, including large genomic islands likely to contribute to virulence and host specificity. (nih.gov)
By looking at our completed sequence, it is predicted that our genome consists of 30,000 to 45,000 genes in each of our cells. (probe.org)
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)
Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. (biomedcentral.com)
10-5) to sequences in GenBank's non-redundant databases, indicating that a large proportion of novel genes are expressed in Heliconius male accessory glands. (ku.edu)
Dear Galaxy, I have the results for the sequence retrieval for Insulator regions in the human genome and I am having difficulty in comprehending the upper and lower case associated with my sequences.I know it for sure that they are regions which do not in any way overlap with exons or introns and are that between any 2 genes. (usegalaxy.org)
This DNA sequence contained in a genome contains the complete code that determines which genes and proteins will be present in human cells. (ubc.ca)
For instance, as a first step in understanding the genomic code we have learnt that the human genome is made of 3.2 billion nucleotide bases (of which there are four types: A, C, T, G). It is thought that over 30,000 genes are encoded by this sequence. (ubc.ca)
Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. (inrae.fr)
Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. (inrae.fr)

An array of protein tandem repeats is defined as several (at least two) adjacent copies having the same or similar sequence motifs. (wikipedia.org)
Repetitive units of protein tandem repeats are considerably diverse, ranging from the repetition of a single amino acid to domains of 100 or more residues. (wikipedia.org)
The degree of similarity can be highly variable, with some repeats maintaining only a few conserved amino acid positions and a characteristic length. (wikipedia.org)
Highly degenerate repeats can be very difficult to detect from sequence alone. (wikipedia.org)
Examples of disordered repetitive sequences include the 7-mer peptide repeats found in the RPB1 subunit of RNA polymerase II, or the tandem beta-catenin or axin binding linear motifs in APC (adenomatous polyposis coli). (wikipedia.org)
Tandem repeats with short repetitive units (especially homorepeats) are more frequent than others. (wikipedia.org)
Protein tandem repeats can be either detected from sequence or annotated from structure. (wikipedia.org)
Theoretically, whenever repeats longer than the reads are present, assemblies are limited within the boundaries of repetitive elements. (biomedcentral.com)
Hello Amit, The genomic sequences hosted on Galaxy are from UCSC and according to their convention repeats from RepeatMasker and Tandem Repeats Finder (with a period of 12 or less) are shown in lower case and non- repeating sequence is shown in upper case. (usegalaxy.org)
Ectopic recombination is typically mediated by sequence similarity at the duplicate breakpoints, which form direct repeats. (ipfs.io)
Although tandem repeats are now being recognized as essential components in chromosome structure and function, it has often been considered sufficient to know the consensus sequence and copy number of such repeats. (uconn.edu)
The capture of an entire array within P1 clones allowed us to generate sub-clones of linked repeats and non-repeat sequences. (uconn.edu)

Secondly, non-adapter-related repetitive sequences were found in most reads, often at the same end of the read, comprising one G-quadruplex sequence and its reverse complement. (news-medical.net)
Our results indicate that even in the "simple" case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone. (biomedcentral.com)
Initial analysis includes: evaluation of reads quality and alignment statistics, samples normalization using internal controls or computational methods, normalized read counts, assessment of sample similarity (principal component analysis PCA plot), differential gene expression, a link to a University of California Santa Cruz (UCSC) genome browser session for all normalized datasets, gene set enrichment analysis (GSEA), gene ontology (GO) terms and pathway enrichment analysis, and motif discovery. (mssm.edu)
Initial analysis includes: evaluation of reads quality and alignment statistics, samples normalization using internal controls or computational methods, a link to a UCSC genome browser session for all normalized datasets, assessment of sample similarity (PCA plot), heat map of promoter activity estimates, identification of alternative promoter usage across conditions, GSEA, and GO terms and pathway enrichment analysis. (mssm.edu)
The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. (inrae.fr)

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)
A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. (inrae.fr)
Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. (inrae.fr)

These periodic sequences are generated by internal duplications in both coding and non-coding genomic sequences. (wikipedia.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)
Replication slippage is an error in DNA replication that can produce duplications of short genetic sequences. (ipfs.io)
Assembly issues are anticipated in genome regions containing segmental duplications (SDs) since they are repeated sequences with higher pairwise similarity. (nicotinic-receptor.com)

As a result, sequence divergence is usually higher when comparing viral strains compared to quasispecies. (biomedcentral.com)
The similarity of strains ranged from 80% to 95%, highlighting the horizontal transference of these microorganisms. (scirp.org)
These bacteriophages appear to be most similar to bacteriophages that infect Pseudomonas and Ralstonia rather than Enterobacteriales bacteria by protein similarity, however, we were only able to detect infection of Erwinia and the closely related strains of Pantoea . (frontiersin.org)

The complete genomic sequence of Pseudomonas syringae pv. (nih.gov)
Full experimental details backed up the published genomic sequence of SARS-CoV-2, but not so that of the RaTG13. (news-medical.net)
In this study, the complete genomic sequence of Fusarium equiseti D25-1 was determined using multiple sequencing platforms. (researchsquare.com)

As a "rule of thumb", short repetitive sequences (e.g. those below the length of 10 amino acids) may be intrinsically disordered, and not part of any folded protein domains. (wikipedia.org)
This "mitogenome" generally has short repetitive non-coding sequences, normally within a single control region (CR). (biomedcentral.com)

Next-generation sequencing (NGS) approaches have surpassed Sanger for generating long viral sequences, yet how variants affect NGS de novo assembly remains largely unexplored. (biomedcentral.com)
For many years, Sanger sequencing has been used to complement classical epidemiological and laboratory methods for investigating viral infections [ 1 ]. (biomedcentral.com)
In both scenarios, overlaps between sequences (Sanger or next-generation sequencing, NGS) have been used to assemble full-length mitogenomes. (biomedcentral.com)

Nucleotide sequence homologies suggest that two opioid peptide precursors, proenkephalin and prodynorphin, may have arisen by duplication from a common ancestral gene. (elsevierpure.com)
The method's focus is to globally detect mass differences, not to assign peptide sequences or modifications to individual spectra. (lu.se)
The goal is to assign acquired spectra to known peptide sequences and potential co- and post-translational modifica- tions. (lu.se)

In proteins, a "repeat" is any sequence block that returns more than one time in the sequence, either in an identical or a highly similar form. (wikipedia.org)
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)
Many extracellular proteins with highly specific and repetitive sequences (keratins, collagens etc.) cluster clearly confirming the accuracy of the clustering method. (unito.it)
Proteins with a more complex structure with multiple domains (catalytic, extracellular, transmembrane etc.), even if classified very similar according to sequence similarity and function (aquaporins, cadherins, steroid 5-alpha reductase etc.) showed different clustering according to amino acid content. (unito.it)
Yet we have also discovered that over 50% of the human genome is repetitive sequence that does not code for any proteins and the function of this large portion of "junk" DNA is still puzzling scientists. (ubc.ca)

LN 278-280: Is there a possibility of KoRV insertion into homologous/repetitive elements with the genome? (peerj.com)
We have utilized a lambda Charon 4A human genomic library to isolate recombinant clones harboring a highly conserved c-src locus containing nucleotide sequences homologous to the transforming gene of Rous sarcoma virus (v-src). (tmu.edu.tw)
Human c-src sequences homologous to the entire v-src region are present in a 20-kilobase region that contains 11 exons as determined by restriction mapping studies utilizing hybridization to labeled DNA probes representing various subregions of the v-src gene and by preliminary DNA sequencing analyses. (tmu.edu.tw)

These results call for careful interpretation of contigs and contig numbers from de novo assembly in viral deep sequencing. (biomedcentral.com)

Many retrogenes display changes in gene regulation in comparison to their parental gene sequences, which sometimes results in novel functions. (ipfs.io)
Thus, we had to manually predict both gene sequences and orthology/paralogy relationships. (nicotinic-receptor.com)

OLC methods involve determining overlaps by performing a series of pair-wise sequence alignments. (biomedcentral.com)
In our case clustering by sequence and amino acid content overlaps. (unito.it)

Two large groups of scientists published the first analyses of this human genome sequence in the February 2001 issues of the journals Nature [1] and Science [2]. (ubc.ca)

Structural similarity can help to identify repetitive patterns in sequence. (wikipedia.org)

For instance, the largest contig contains genetic material with 98% similarity to the full-length mitochondrial sequence of the Chinese rufous horseshoe bat ( Rhinolophus sinicus ), an unlikely event since a complete assembly of such a sequence is typically interrupted by stop codons. (news-medical.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)

The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. (inrae.fr)

The dataset that has been published in support of the RaTG13 genome, almost 30 kb long, has been found inadequate to reproduce the sequence or the experimental observations based on this dataset. (news-medical.net)
While the dataset is unique and contains much information beyond the fragmented coronavirus sequence, not much is known about how it was generated. (news-medical.net)
I am using a whole exome sequencing dataset to look for potential pathogenic mutations. (usegalaxy.org)

We found that, while there is an inverse correlation between distance and repeat similarity, there is also a cline of variability, with the most haplotypes appearing at the distal end of the locus and the fewest at the proximal end. (uconn.edu)
Finally, it was confirmed that there are distinct functional groups within this complex repetitive locus. (uconn.edu)

The HGP was an initiative started in the early 1990's that has involved the efforts of hundreds of scientists to generate high-quality reference sequence for the 3 billion base pairs of nucleotide sequence that make up the human genome. (ubc.ca)
The nucleotide sequence of a 6.8-kb region of human DNA containing the proenkephalin gene and flanking regions is reported. (elsevierpure.com)

Hi, Using the interval file which you used to fetch fasta sequences, you'll be able to fetch human-chimp alignments. (usegalaxy.org)
You can display matches as multiple alignments or group them by degree of similarity in a tree view. (cshl.edu)

Like the librarian putting warning labels on certain books, these enzymes leave the genetic sequence untouched by appending small carbon packets (methyl groups) to the DNA molecule, which means they are operating epigenetically. (bionity.com)
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)

Over 375 repetitive extragenic palindromic sequences unique to Pss B728a when compared with Pst DC3000 are widely distributed throughout the chromosome except in 14 genomic islands, which generally had lower GC content than the genome as a whole. (nih.gov)
To better understand the karyotype organization in Melipona and the relationship among the subgenera, we mapped repetitive sequences and analyzed previously reported cytogenetic data with the aim to identify cytogenetic markers to be used for investigating the phylogenetic relationships and chromosome evolution in the genus. (karger.com)

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)
Regardless of the slight differences, all organisms use the same coding mechanism for translating the code into amino acid sequences. (rationalwiki.org)

The structural organization of the human proenkephalin gene exhibits striking similarities to the organization of the human pro-opiomelanocortin (POMC) gene. (elsevierpure.com)

By comparing sequences from these different model organisms, scientists gain a better understanding of the important pieces of code in genomic DNA sequence since conservation of sequences between two organisms that diverged phylogenetically millions of years ago, like humans and worms, implies that the conserved sequence is important for function. (ubc.ca)

A considerable degree of similarity exists between the organization of the human c-src gene and that of the corresponding chicken c-src gene with respect to exon size and number. (tmu.edu.tw)

BCC), among hospitalized patients at hospital A. Most sequences of B. stabilis for all eight clinical (seven from blood patients had undergone ultrasound-guided procedures during and one from ascites fluid) and three product isolates collected their admission. (cdc.gov)

A recent study to understand and improve Pfam coverage of the human proteome showed that five of the ten largest sequence clusters not annotated with Pfam are repeat regions. (wikipedia.org)

We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. (biomedcentral.com)

DNA is a polymer, a repetitive sequence of four molecules, which I will only refer to by their one-letter abbreviations, A, G, C, and T. The human genome sequence is simply the sequence of these four molecules in DNA from all our chromosomes. (probe.org)

Many scientists mention the genome sequence of this bat CoVs, RaTG13, as being part of the ancestral descent of the current virus. (news-medical.net)
By reading the sequence of the human genome, scientists hope to gain an understanding of the underlying code that determines how a complex biological system, such as a human cell, acts and reacts. (ubc.ca)
The HGP started at a meeting of scientists during which the value of knowing the genome sequence of an organism was recognized. (ubc.ca)
However, this first draft was not considered to be complete by scientists because of significant gaps in the sequences (this draft was 90% complete). (ubc.ca)
For scientists, the high-quality reference sequence publicly released in April 2003 represents the first real step to having "finished" human sequence on hand (this draft represents sequence information that is considered to be 99% complete) [3]. (ubc.ca)
With genome sequence in-hand scientists are now more effectively able to study gene function and explore new areas of research such as how human variation contributes to different diseases worldwide. (ubc.ca)
The sequence of B1 is so similar to Alu that evolutionary scientists have concluded both elements derived from the same molecule (the signal recognition particle ) at different times in evolutionary history. (reasons.org)
There, view your results alongside the results other scientists have found and published for the sequence. (cshl.edu)

It was also found that proximity to non-repeat sequences did not significantly increase variability. (uconn.edu)
To further test the effects of transposon-aided gene amplifications on genome evolution and architecture, the repetitive fraction of the significantly expanded genome of the banana pathogen, Pseudocercospora fijiensis , was analyzed in greater detail. (biomedcentral.com)

Results: We successfully sequenced 933 ESTs clustering into 371 unigenes from H. erato and 1033 ESTs clustering into 340 unigenes from H. melpomene. (ku.edu)
I downloaded the BED file from the website pointed by you, and fetched sequences successfully. (usegalaxy.org)

But, from the design perspective, if we need Alu elements in certain locations, mice (with whom we share a lot of common biology) will need a similar sequence in the same location. (reasons.org)

These major accomplishments in genome sequencing provide a wealth of information that aid in the understanding of basic biological processes. (ubc.ca)

The researchers found that using the available data, they were unable to detect any contiguous sequences larger than 17 kb, using several different settings. (news-medical.net)

To date, mtDNA sequences have been generated for hundreds of thousands of specimens in many vertebrate species [ 8 ]. (biomedcentral.com)
As a first step in pursuing this research, we report the generation and analysis of expressed sequence tags (ESTs) from the male accessory gland of H. erato and H. melpomene, species representative of the two mating systems present in the genus Heliconius. (ku.edu)
2016). Latent paralogous variation may possibly bias interpretations of sequence diversity and haplotype structure (Hurles 2002), and ancestral duplication followed by differential losses along separate lineages may result in a nearby phylogeny that's discordant using the species phylogeny (Goodman et al. (nicotinic-receptor.com)
Nonfunctional DNA sequences that have the same location in many species prove that their DNA was "inherited" through the process of evolution. (reasons.org)
Alu elements are nonfunctional DNA sequences that have the same location in many species. (reasons.org)

Results were compared to those based on sequence similarities. (unito.it)

Non-histone sequences were shown to contain direct and indirect evidence of mobile elements. (uconn.edu)

Build vocabulary and increase fluency and high-frequency word recognition with easy-to-read, repetitive text. (discountschoolsupply.com)
Management and analysis of high-throughput sequence data for infectious animal diseases. (exeter.ac.uk)
LN 185-187: Do the LTRs of any other ERVs share high sequence identity with those of KoRV, which might lead to an over-estimation of KoRV sites? (peerj.com)
These sequences undergo a process known as concerted evolution, which is the nonindependent evolution of repetitive DNA sequences resulting in a high sequence similarity of repeating units. (uconn.edu)

Structure-based methods instead take advantage of the modularity of available PDB structures to recognize repetitive elements. (wikipedia.org)
Evolutionists conjecture that repetitive elements like Alu and B1 are placed randomly in the genome and then evolve new function based on where they are placed. (reasons.org)
Evolution can't readily explain how the sequences came to be in the same places because the Alu elements and B1 elements arose supposedly after the lines diverged. (reasons.org)

These approaches depend on sequence databases that are used by the engines to match real spectra to theoretical in silico spectra. (lu.se)

The focus of the current paper is on the accuracy of the data on these sequences. (news-medical.net)
Custom analysis includes: gene expression modules, data integration (e.g., assay for transposase-accessible chromatin-sequencing or ATAC-seq and chromatin immunoprecipitation -sequencing or ChIP-seq), data integration with publicly available resources (e.g. (mssm.edu)
If you work with one of the sample sequences, you can also export data to a genome hub such as Phytozome. (cshl.edu)
DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). (inrae.fr)

Browsers use boxes and lines to represent exons and introns, and allow you to zoom in and out of your DNA sequence. (cshl.edu)

Comparison of the complete genome sequences of Pseudomonas syringae pv. (nih.gov)

The proposed method is novel because it works independently of protein sequence databases and without any prior knowledge about modifica- tions. (lu.se)
PTMs from this list in conjunction with a protein sequence and a few precursor masses. (lu.se)

The race to publish human genome sequence information was fuelled by competition between research from the publicly funded HGP and the privately owned company, Celera Genomics. (ubc.ca)

The first and primary goal of the HGP was to map and sequence the entire human genome. (probe.org)
Officially, funding for the project began in the 1990 with the goal of sequencing the human genome by 2005. (ubc.ca)
This first working draft of the human genome sequence was hailed with much excitement and fanfare as the "completion of the human genome" in the media. (ubc.ca)
The mouse genome is about 10% smaller than the human genome, owing to a lower repetitive DNA content. (inrae.fr)
alu family repetitive sequences are present within several human c-src introns. (tmu.edu.tw)

According to the new study, Dnmt1 has, contrary to previous assumptions, the ability to target specific sequences in the mouse genome and attach methyl marks to them outside of its maintenance duties. (bionity.com)
Is there a possibility that some of the sequences obtained are non-specific to KoRV, but may be from other ERV present in the koala? (peerj.com)

The absence of a single, option order favors selection (b): underlying assembly complications triggered by higher sequence identity and higher density of repetitive sequences. (nicotinic-receptor.com)

The variation in this preference along the length of nucleosomal DNA and the intrinsic sequence-dependent bendability of DNA implies that strong translational settings can also occur. (nature.com)

The total repetitive sequence length was 1,713,918 bp, accounting for 4.2033% of the genome. (researchsquare.com)
I tried to retrieve a set of 20 bp length genomic sequences using the UCSC Table Browser, using. (usegalaxy.org)

Anatomy21

Organisms22

Diseases5

Chemicals and Drugs57

Analytical, Diagnostic and Therapeutic Techniques and Equipment36

Phenomena and Processes128

Disciplines and Occupations3

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture3

Information Science8

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Geographicals1

Genomes10

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Repeats12

Reads5

Whole-genome5

Duplications4

Strains3

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Short repetitive2

Sanger3

Peptide3

Proteins5

Homologous3

Novo assembly1

Gene sequences2

Overlaps2

Analyses1

Patterns1

Mitochondrial1

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Dataset3

Locus2

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Alignments2

Genetic2

Chromosome2

Amino2

Structural1

Organisms1

Organization1

Isolates1

Clusters1

Considerable1

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Scientists8

Significantly2

Successfully2

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Results1

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High4

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Length2