Sequences sequence homology. Medical search. Frequent questions

The term "percent homology" is often used to mean "sequence similarity", that is the percentage of identical residues (percent identity), or the percentage of residues conserved with similar physicochemical properties (percent similarity), e.g. leucine and isoleucine, is usually used to "quantify the homology. (wikipedia.org)
This involves that the term "percent homology" is a misnomer. (wikipedia.org)
The two proteins demonstrate 76 percent homology in their amino acid sequences. (quizlet.com)

If I'm not mistaken, you're giving a .fasta file of the sequence that you want to model, and an alignment.filt file containing an alignment of that sequence with each of the homologs you wish to model against. (rosettacommons.org)
By using sequence alignment of herpesviruses homologs, we identified conserved amino acids in the putative pUL105 ATP binding site and in the putative pUL70 zinc finger pattern. (frontiersin.org)
Low sequence conservation and lack of functional annotations make it difficult to identify homologs of mammalian lncRNAs in other vertebrates. (sissa.it)

Alignments of multiple sequences are used to indicate which regions of each sequence are homologous. (wikipedia.org)
Sequences are either homologous or not. (wikipedia.org)
As with morphological and anatomical structures, sequence similarity might occur because of convergent evolution, or, as with shorter sequences, by chance, meaning that they are not homologous. (wikipedia.org)
Homologous sequence regions are also called conserved. (wikipedia.org)
Homologous sequences are orthologous if they are inferred to be descended from the same ancestral sequence separated by a speciation event: when a species diverges into two separate species, the copies of a single gene in the two resulting species are said to be orthologous. (wikipedia.org)
Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins. (rochester.edu)

The submitted sequences may reflect pathogen evolution during the course of the outbreak but the majority of the encoded proteins from these genomes may be identical to each other. (stackexchange.com)
Because a non-redundant protein sequence may be found in RefSeq genomes from multiple species, the organism information provided on the protein record reflects the lowest-common taxonomic node ranging from the genus species level to super-kingdom . (stackexchange.com)
Indeed, starting from ~2,800 mouse lncRNAs we could predict that between 4 and 11% present conserved sequence fragments in fish genomes. (sissa.it)
We believe this study will result useful as a reference to analyze the conservation of lncRNAs in newly sequenced genomes and transcriptomes. (sissa.it)
This problem is magnified in organisms that have their genomes sequenced for the first time ( Fig. 1c ). (nature.com)

Such partial homology may result from a gene fusion event. (wikipedia.org)
citation needed] Given their tremendous importance for biology and bioinformatics, orthologous genes have been organized in several specialized databases that provide tools to identify and analyze orthologous gene sequences. (wikipedia.org)
of the 5 S rRNA gene sequences of rice variety IR20 and 17 S and 25 S rRNA gene sequences of rice variety Mangetsumochi revealed the presence of 39 hexa, 4 hepta, and 2 octa nucleotide homologies between 5 S and 17 S rRNA genes and 48 hexa, 11 hepta, 6 octa and 1 nano nucleotide homologies between 5 S and 25 S rRNA genes. (iisc.ac.in)
A set of 34 genes clustered around the rifK gene encoding AHBA synthase were defined by sequencing all but 5 kilobases (kb) of a 95 kb contiguous region of DNA from A. mediterranei. (nih.gov)
Previous studies indicate that the rat B-myc gene contains a single exon which shows 77% nucleotide homology to the second exon of the rat c-myc gene. (mssm.edu)
Nucleotide analysis of B-myc coding and non-coding sequences suggests that it may be a functional gene evolved by selective duplication of part of the second c-myc exon. (mssm.edu)
We show that the mouse putative pS2 protein sequence and the physiological pattern of expression of the mouse pS2 gene are well conserved. (xenbase.org)
Estrogen-responsive element of the human pS2 gene is an imperfectly palindromic sequence. (xenbase.org)
Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species. (bvsalud.org)

Homology among DNA, RNA, or proteins is typically inferred from their nucleotide or amino acid sequence similarity. (wikipedia.org)
We have extended our studies to encompass intrinsically disordered proteins, and are using the sequences of those proteins as an added resource in the study of folding and stability in proteins. (rochester.edu)
Sequence-specific dynamic information in proteins. (rochester.edu)

homology modeling- Error: length mismatch between sequence and alignment. (rosettacommons.org)
Member Site › Forums › Rosetta 3 › Rosetta 3 - Applications › homology modeling- Error: length mismatch between sequence and alignment. (rosettacommons.org)
What this excerpt is doing is checking that each sequence in the alignment is the same length. (rosettacommons.org)
A computational evaluation of the lncRNAs through systematic conservation analyses of both sequences as well as their genomic architecture is required.Results: Our results show that a subset of mouse candidate lncRNAs could be distinguished from random sequences based on their alignment with zebrafish phastCons elements. (sissa.it)
Beyond Supersecondary Structure: Physics-Based Sequence Alignment. (rochester.edu)
Para o alinhamento das seqüências, referentes a região NS5b, foi utilizado o programa Clustal W (Clustal W Multiple Sequence Alignment Program, v1.7, June 1997) e a árvore filogenética foi gerada pelo método Neighbor Joining. (usp.br)
Areas that will be covered include: sequence databases, pairwise and multiple sequence alignment, homology searches in sequence databases and subcellular localization prediction. (lu.se)

begingroup$ The Serre spectral sequence is functorial. (mathoverflow.net)
It is true that each element of the group gives a map of spectral sequences. (mathoverflow.net)
If you construct the Serre spectral sequence in the usual way, there is a non-equivariantly inconsequential choice of base point in the base space. (mathoverflow.net)
You do not get to collate your actions one element of the group at a time into an algebraically meaningful action of the group on "the" spectral sequence. (mathoverflow.net)
Then there is an equivariant Serre spectral sequence, developed by Moerdijk and Svensson: The equivariant Serre spectral sequence. (mathoverflow.net)

Significant similarity is strong evidence that two sequences are related by evolutionary changes from a common ancestral sequence. (wikipedia.org)
Based on the definition of homology specified above this terminology is incorrect since sequence similarity is the observation, homology is the conclusion. (wikipedia.org)
Significant sequence similarity and shared functional domains indicate that these two genes are orthologous genes, inherited from the shared ancestor. (wikipedia.org)
The degree of similarity between sequences. (bvsalud.org)

9] P. Baum and R. Douglas , K-homology and index theory , Operator algebras and applications, Proc. (numdam.org)

My sequence had 241 amino acids and I found a lot of sequences with 100% identity, 100% cover and 0 E-value exactly the same as my sequence but with different IDs. (stackexchange.com)
We also constructed, by homology modeling, a theoretical structure of the pUL105 N-terminal domain which indicates that the mutated conserved amino acids in this domain could be involved in ATP hydrolysis. (frontiersin.org)

There was no hybridization between 5 S rRNA and 5.8 S rRNA genes, though a hexa and a hepta nucleotide sequence homologies are found between them. (iisc.ac.in)
This suggested that \geq1 hepta nucleotide sequence homol. (iisc.ac.in)
Simmonds P . SSE: a nucleotide and amino acid sequence analysis platform. (microbiologyresearch.org)
A proportion of these will alter protein sequences, the most common of which is the non-synonymous single nucleotide polymorphism (nsSNP). (biomedcentral.com)

In summary, we show that interesting genomic regions in zebrafish could be marked based on their sequence homology to a mouse lncRNA, overlap with ESTs and proximity to genes involved in nervous system development.Conclusions: Conservation at the sequence level can identify a subset of putative lncRNA orthologs. (sissa.it)
Furthermore, comparative genomics through BES can be used for identifying positional candidate genes from QTL mapping studies, aid in future assembly of a reference genome sequence and elucidating sequence content and complexity in the rainbow trout genome. (biomedcentral.com)
In the present report we have compared and contrasted structure- and sequence-based methods of prediction to over 5500 genes carrying nearly 24,000 nsSNPs, by employing an automatic comparative modelling procedure to build models for the genes. (biomedcentral.com)
These genes similarly contain sequences that encode for the HMG-box domain, which is responsible for the sequence-specific DNA-binding activity. (thermofisher.com)

In recent work we developed the first bioinformatic representation of protein dynamics, and are currently using this tool, in combination with earlier studies of the static physical properties of amino acid sequences, to elucidate basic mechanisms of protein folding. (rochester.edu)
In earlier work, we have applied novel bioinformatic methods to the comparison of protein sequences and protein structures, and used the resulting data to address problems at the foundations of bioinformatics. (rochester.edu)

Because recombinant antibody production involves sequencing the antibody light and heavy chains, it is a highly controlled and reliable process. (cellsignal.com)

Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. (wikipedia.org)
Major technological advances in affordable nucleic acid sequencing have allowed for an explosion of sequencing data and molecular tools available for researchers in biological sciences. (lu.se)

The similar protein-coding neighborhood and transcriptional information about the conserved candidates provide support to the hypothesis that they share functional homology. (sissa.it)

However, the lack of a reference genome sequence hampers research progress for both academic and applied purposes. (biomedcentral.com)
In order to enrich the genomic tools already available in this species and provide further insight on the complexity of its genome, we sequenced a large number of rainbow trout BAC-end sequences (BES) and characterized their contents. (biomedcentral.com)
The discovery of specific repeat elements will facilitate analyses of sequence content (e.g. for SNPs discovery and for transcriptome characterization) and future genome sequence assemblies. (biomedcentral.com)
Real-Time Genome Sequencing of Resistant Bacteria Provides Precision Infectio. (slideshare.net)
The recent sequencing of the human genome has provided a wealth of information detailing several million genetic variations between individuals. (biomedcentral.com)

The most identifiable category of SNP is the small proportion (less than 1%) that change protein sequence, the most common of which is the non-synonymous SNP. (biomedcentral.com)
Protein sequence design and its applications. (ncbs.res.in)

Homolog detection using global sequence properties suggests an alternate view of structural encoding in protein sequences. (rochester.edu)
NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection. (ncbs.res.in)

The first rainbow trout repeat elements database (INRA RT rep1.0) containing 735 putative repeat elements was developed, and identified almost 59.5% of the BES database in base-pairs as repetitive sequence. (biomedcentral.com)

Many sequences-particularly bacterial sequences-are identical between various different species so having a separate RefSeq entry for each of them would be inefficient. (stackexchange.com)

When confronted with the task of finding homology to large numbers of sequences, database searching tools such as Blast and Fasta generate prohibitively large amounts of information. (aaai.org)
Note that you should also make sure that each reference sequence in your pair, ignoring gaps, matches the input sequence from the .fasta. (rosettacommons.org)

Orthologous sequences provide useful information in taxonomic classification and phylogenetic studies of organisms. (wikipedia.org)
These resources employ approaches that can be generally classified into those that use heuristic analysis of all pairwise sequence comparisons, and those that use phylogenetic methods. (wikipedia.org)
Lu L , Li C , Hagedorn CH . Phylogenetic analysis of global hepatitis E virus sequences: genetic diversity, subtypes and zoonosis. (microbiologyresearch.org)

Partial homology can occur where a segment of the compared sequences has a shared origin, while the rest does not. (wikipedia.org)

This is not to be confused with conservation in amino acid sequences, where the amino acid at a specific position has been substituted with a different one that has functionally equivalent physicochemical properties. (wikipedia.org)
But having a short sequence of 241aa in several sequence might indicate good conservation (maybe it is a domain? (stackexchange.com)

Two organisms that are very closely related are likely to display very similar DNA sequences between two orthologs. (wikipedia.org)
Conversely, an organism that is further removed evolutionarily from another organism is likely to display a greater divergence in the sequence of the orthologs being studied. (wikipedia.org)

A new type of RefSeq protein record which represents non-redundant protein sequences was introduced in mid-2013. (stackexchange.com)

One of the most important rules for reducing the amount of output is to linlit the number of overlapping matches to the same region of the query sequence. (aaai.org)
Show us your query sequence and a few of the redundant results. (stackexchange.com)

BES analyses identified 6,848 simple sequence repeats (SSRs), of which 3,854 had high quality flanking sequences for PCR primers design. (biomedcentral.com)

Sequence analysis of this clone confirmed the presence of one single coding exon. (mssm.edu)

Sequence comparison methods were first pioneered in the COGs database in 1997. (wikipedia.org)
I had a protein Refseq ID and I PSI-BLASTed this sequence against Refseq database. (stackexchange.com)
We all know that the Refseq is a Reference sequence database and it shouldn't have redundancy. (stackexchange.com)
Is it really a Reference sequence database? (stackexchange.com)

Few and small studies have been reported about multigene testing usage by massively parallel sequencing in European cancer families. (cancerindex.org)

We predict organismal metabolic networks using sequence homology and a global metabolic network constructed from all available organismal networks. (nature.com)
We show, however, that when homology is used with a global metabolic network one is able to predict organismal metabolic networks that have enhanced network connectivity. (nature.com)

Although it remains difficult to define strict criteria for distinguishing between virus subtypes, and is not within the remit of the International Committee on Taxonomy of Viruses (ICTV), the use of agreed reference sequences will bring clarity and stability to researchers, epidemiologists and clinicians working with HEV. (microbiologyresearch.org)
Proposed reference sequences for hepatitis E virus subtypes. (microbiologyresearch.org)

In other iterations and after adjusting format options, I got this redundancy with other sequences from other species. (stackexchange.com)

Beyond supersecondary structure: the global properties of protein sequences. (rochester.edu)

For over 40% of the nsSNPs, structure-based methods predicted which of these sequence changes are likely to either disrupt the structure of the protein or interfere with the function or interactions of the protein. (biomedcentral.com)

Global informatics and physical property selection in protein sequences. (rochester.edu)

Approximately 55% of the BES reads (97,846) had more than 100 base pairs of contiguous non-repetitive sequences. (biomedcentral.com)

An automatic way of making most of the decisions a trained sequence analyst would make was developed by means of a rule-based expert system combined with an algorithm to avoid noninformative biased residue composition matches. (aaai.org)

The results found relevant by the system are presented in a very concise and clear way, so that the homology can be assessed with minimum effort. (aaai.org)

This set of rules proved to be robust for most cases and gives high fidelity separation between real homologies and spurious matches. (aaai.org)

I solved the problem by setting 'unwrap text' setting in my text editor and writing sequences in one line. (rosettacommons.org)

While sequence homology has been a standard to annotate metabolic networks it has been faulted for its lack of predictive power. (nature.com)

Sequence of the pS2 mRNA induced by estrogen in the human breast cancer cell line MCF-7. (xenbase.org)

Each member of the p120ctn family consists of a central domain consisting of nine armadillo (arm) repeats broken by a wedge between repeats 5 and 6 plus N- and C-terminal sequences that differ substantially between family members ( Pokutta and Weis, 2007 ). (jneurosci.org)

My question is, what sequences are being compared to produce this message. (rosettacommons.org)

Anatomy11

Organisms31

Chemicals and Drugs85

Analytical, Diagnostic and Therapeutic Techniques and Equipment37

Phenomena and Processes91

Disciplines and Occupations1

Technology, Industry, Agriculture2

Information Science6

Health Care2

Percent homology3

Homologs3

Homologous6

Genomes5

Gene9

Proteins3

Alignment7

Spectral5

Similarity4

Proc1

Amino acids2

Nucleotide4

Genes4

Bioinformatic2

Antibody1

Biological2

Transcriptional1

Genome5

Protein sequence2

Detection2

Putative1

Bacterial1

Fasta2

Phylogenetic3

Occur1

Conservation2

Orthologs2

Represents1

Query sequence2

Analyses1

Analysis1

Database4

Studies1

Predict2

Reference2

Species1

Properties1

Methods1

Global1

Base1

Means1

Found1

High1

Problem1

Lack1

Human1

Domain1

Question1