Secondary alignment position specific scoring matrices. Medical search. Frequent questions

Przybylski D. and Rost,B. (2002) Alignments grow, secondary structure prediction improves. (wikipedia.org)
Jones D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. (wikipedia.org)
Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. (keywen.com)
As a next step we compared the different results of the secondary structure prediction tools JPred and PsiPred. (tu-muenchen.de)

PredictProtein (PP) is an automatic service that searches up-to-date public sequence databases, creates alignments, and predicts aspects of protein structure and function. (wikipedia.org)
SEquence-structure alignment with 123D+ server. (keywen.com)
Sequence-structure alignments Sequence-structure alignments were generated and tested both at the sequence level as well as at the 3D level. (keywen.com)
The input to the program was the alignment between the target sequence and template structure(s). (keywen.com)
Finally, to our knowledge, the presented structure-search machinery is the only one to permit arbitrary combinations of amino-acid-type constraints, secondary structure constraints, distance constraints, and sequence separation constraints. (biomedcentral.com)
Besides, we looked additional at the position specific scoring matrix (PSSM) for ouer sequence. (tu-muenchen.de)
In contrast to PAM and BLOSOUM, the PSSM contains a specific substitution rate for each position in the sequence. (tu-muenchen.de)
As a next step we created a multiple alignment which contains the HEXA sequence and 9 other mammalian homologous sequences from uniprot. (tu-muenchen.de)
Initially, we performed Multiple Sequence Alignment (MSA) of all species followed by Position Specific Scoring Matrix (PSSM) for both loci to achieve a percentage of discrimination among species. (biomedcentral.com)
Structure-based sequence alignments were generated and the residues in the helix-helix interfaces were analyzed. (biomedcentral.com)
The multiple sequence alignment provides more information than sequence itself. (biomedcentral.com)

Therefore, the PSSM is more position specific than PAM or BLOSOUM. (tu-muenchen.de)
In this paper, we report a novel computational approach combining fuzzy local ternary pattern (FLTP), Position-Specific Scoring Matrix (PSSM), and rotation forest (RF) to identify DTIs. (imrpress.com)
PSSMCOOL contains the computation of various features from Position Specific Scoring Matrix (PSSM). (osuosl.org)

The predominant molecules of this extracellular matrix are type 1 and type 3 collagen, with a small amount of type 4 collagen at the basement membrane. (medscape.com)
We also examined healthy porcine cartilage explants treated with physiologic doses of leptin, alone or in combination with IL-1α and palmitic and oleic fatty acids, to determine the effects of leptin on cartilage extracellular matrix homeostasis. (biomedcentral.com)
Physiologic doses of leptin, in the presence or absence of IL-1α and fatty acids, did not substantially alter extracellular matrix homeostasis in healthy cartilage explants. (biomedcentral.com)
Physiologic levels of leptin do not alter extracellular matrix homeostasis in healthy cartilage, suggesting that leptin may be a secondary mediator of osteoarthritis pathogenesis. (biomedcentral.com)

Afterwards, we looked at the values of the substitution matrices PAM1, PAM250 and BLOSSUM62. (tu-muenchen.de)
In this case, the substitution of Phenylalanine to Serine has low values that are nearer to the values for the rarest subsitution for all three matrices. (tu-muenchen.de)
In this case the substitution rate for Phenylalanine to Serine at this position is very low and near the value for the rarest substitution. (tu-muenchen.de)
This means that this substitution at this position is likely very uncommon which indicates that this substitution has bad effects as consequence. (tu-muenchen.de)

Therefore, according to PAM1 and PAM250 a mutation at this position will almost certainly cause structural changes which can affect functional changes. (tu-muenchen.de)

We think that a drastical change of the protein structure and its function is unlikly because the mutation does not affect a secondary struture element. (tu-muenchen.de)

Designed for use with counts, CA is based on decomposition of a chi-squared residual matrix and does not require log-transformation of scRNAseq counts. (ne.jp)
We propose to resolve this dilemma by using a nonmetric analogue of spectral matrix decomposition, namely, the decomposition of the proximity matrix into a sum of equally-sized matrices, restricted only to display an order-constrained patterning, the anti-Robinson (AR) form. (scirp.org)
We propose an extension of the order-constrained anti-Robinson decomposition of square-symmetric proximity matrices to the analysis of individual differences of three-way data, with the third way representing individual data sources. (scirp.org)

To overcome the host plant defense response, M. phaseolina encodes a significant number of P450s, MFS type membrane transporters, glycosidases, transposases, and secondary metabolites in comparison to all sequenced ascomycete species. (biomedcentral.com)
OBJECTIVES: This study aimed to test the hypothesis that fungal diversity is inversely associated with neighborhood asthma prevalence and identify specific fungal species associated with asthma morbidity. (cdc.gov)

This has a result, that the mutation at this position would not destroy or split a secondary structure element. (tu-muenchen.de)

A subgroup of rice and maize NIPs has small residues in three of the four positions in the ar/R tetrad, resulting in a wider constriction. (biomedcentral.com)
18 The human immune system started generating antibodies specific to residues outside RBD even at the earlier stage of the pandemic. (biorxiv.org)

Once you feel those pages are in good shape, you'll need to harvest them for primary, secondary, and tertiary keywords. (act-on.com)

The adaptation of correspondence analysis for to the integration of multiple tables is similar to the method for single tables with additional matrix concatenation operations. (ne.jp)
Multiple discrete (non-spatial) and continuous (spatial) structures can be fitted to a proximity matrix to increase the information extracted about the relations among the row and column objects vis-à-vis a representation featuring only a single structure. (scirp.org)
However, using multiple discrete and continuous structures often leads to ambiguous results that make it difficult to determine the most faithful representation of the proximity matrix in question. (scirp.org)
Mutations with respect to the Chinese reference were identified by multiple genome alignment. (cdc.gov)

Although the experimental evidence mentioned above linked the TK gene with virulence, its overall specific mechanism of action remains elusive. (biomedcentral.com)
The Rhodopsin family accounts for ~68% of the Ciona GPCR repertoire wherein the LGR-like subfamily exhibits a lineage specific gene expansion of a group of receptors that possess a novel domain organisation hitherto unobserved in metazoan genomes. (biomedcentral.com)

Afterwards we looked at the position of the different mutations and looked at the conservation level on this position. (tu-muenchen.de)
Jensen-Shannon and Grantham scores were computed for mutations in protein-coding genes to evaluate whether they affected protein function. (cdc.gov)

For investigation of prevalence by specific nested PCR, 120 skin specimens were similarly obtained from 120 volunteers. (cdc.gov)

Specific PCR analysis further identified this virus in 2/8 patients with MCC but in only 1/111 controls without MCC. (cdc.gov)
The terroir signature at the macro zone level was revealed using suitable statistical techniques such as the PCA, which is the principal component analysis, and the auto BLSDA, which is the bidirectional orthogonal projection to leaden structures, discrete analysis, to analyze both the transcriptomics, and the metabalomics data matrix. (jove.com)

Altschul S.F. and Gish,W. (1996) Local alignment statistics. (wikipedia.org)
IMPALA: Integrating Matrix Profiles And Local Alignments 1. (animalgenome.org)

We conducted primary and secondary research across 20 diverse companies that recently underwent a digital transformation and found that, regardless of industry, organisations that appointed empowered CDOs-backing them with strong mandates and executive support-exhibited dramatic operational improvement. (deloitte.com)

The structure of the molecules can be incorporated in the alignment. (keywen.com)

The former displays the relation between the row and column objects of the proximity matrix as a graph, with objects represented by nodes and dissimilarities fitted by edges of different length connecting the object nodes. (scirp.org)

This is evident at the subfamily level comparisons since Ciona GPCR sequences are significantly analogous to vertebrate GPCR subfamilies even while exhibiting Ciona specific genes. (biomedcentral.com)

In this case both tools agree and predict at the position of the mutation a coil. (tu-muenchen.de)
10 , 11 Studies attempting to predict the secondary structural elements of this protein indicate one α-helix and, depending on the study, two β-strands. (biorxiv.org)

Therefore, an exchange at this position is very unlikely and a mutation there will almost certainly cause structural changes which can affect functional changes. (tu-muenchen.de)
Therefore, the mutation on this position is highly conserved and a mutation there will cause probably huge structural and functional changes for the protein. (tu-muenchen.de)

impala : search program (searches a database of score matrices, prepared by copymat, producing BLAST-like output). (animalgenome.org)
Your search engine results page (SERP) rank is positioned above your competitors. (act-on.com)

Map2NCBI provides information on markers described by their positions by querying the NCBI database. (osuosl.org)

Currently available in more than select cities and expanding on a global basis throughout Europe, Asia and South America, customers use the Uber app to locate a ride in a matter of minutes, view fares for specific locations, request rides, and also track the location of their reserved vehicle. (lswgold.com)
Yuan, J. The score of a global alignment is the number in the matrix element at the lower right. (forextrading-madeeasy.com)

Proximities are usually collected into a matrix, with rows and columns representing the objects. (scirp.org)

It will probably only changes the coil between two secondary structure elements, but this can sometimes also cause a change of the the following secondary structure. (tu-muenchen.de)
Imagine that the DNA "elements" at each position are mirrored from one strand to the other. (ainews.one)

As our ultimate goal, we seek to extract a small number of matrices in AR form such that their sum allows for a parsimonious, but faithful reconstruction of the total variability among the original proximity entries. (scirp.org)

The PAM-matrices are evolutionary models whereas BLOSUM is based on protein families. (tu-muenchen.de)
Both models are directly comparable for a given proximity matrix because they involve the same number of parameters estimable through least-squares minimization. (scirp.org)

https://www.biorxiv.org/content/10.1101/2021.11.23.469039v1.full.pdf a new algorithm for aligning both reads in a pair simultaneously by fuzzily intersecting the sets of candidate alignment locations for each read. (ne.jp)

For every Λ ⊆ Nn × Nn at most one zero-divisor matrix with its pattern of zero and non-zero entries prescribed by Λ is not in W. (ne.jp)

Cervical ripening is associated with decreased collagen fiber alignment, decreased collagen fiber strength and diminished tensile strength of the extracellular cervical matrix. (medscape.com)

In addition to a general factor for reading competence, we expected gender-stereotypical texts to give rise to gender-specific factors regarding the text content. (springer.com)

the way relates to the dimensionality of the matrix, and the mode to the number of sets of entities the ways correspond to. (scirp.org)

Afterwards we can examine in which secondary structure element and where therein the mutation takes place. (tu-muenchen.de)

Clinical outcomes regarding pain, function and quality of life will be assessed using the Oxford Shoulder Score, Oxford Shoulder Instability Score, Quick DASH, American Shoulder and Elbow Society Score, EQ-5D-5 L and active shoulder range of movement. (biomedcentral.com)

To position the device at valorant ragebot 90, , or degrees: In the Device rotation area, select a button to change the rotation. (lswgold.com)

The mention of specific companies or of certain manufacturers' products does not imply that they are endorsed or recommended by WHO in preference to others of a similar nature that are not mentioned. (who.int)

Most of the plant MIPs that have been investigated are highly specific for water. (biomedcentral.com)

Using voluntary sampling, physiotherapists working in Australia were recruited through advertisements placed in physiotherapy-specific electronic publications and communications and via professional networks. (lswgold.com)

Each AR matrix captures a unique amount of the total variability of the original data. (scirp.org)
Interleave VR is a shoot 'em up for the Oculus Rift that introduces a unique VR-specific mechanic allowing for the comfortable use of third person view POV changhes in fully immersive virtual reality. (interleave-vr.com)

Anatomy21

Organisms6

Diseases9

Chemicals and Drugs63

Analytical, Diagnostic and Therapeutic Techniques and Equipment52

Psychiatry and Psychology1

Phenomena and Processes82

Disciplines and Occupations3

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Structure prediction4

Sequence11

PSSM3

Extracellular matrix4

Substitution4

PAM11

Protein structure1

Decomposition3

Species2

Mutation at this position1

Residues2

Tertiary1

Multiple4

Gene2

Mutations2

Prevalence1

Analysis2

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Molecules1

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