PepServe: a web server for peptide analysis, clustering and visualization

Αλεξανδρίδου, Αναστασία; Dovrolis, Nikolas; Tsangaris, George T.; Nikita, Konstantina S.; Spyrou, George M.

doi:10.1093/nar/gkr318

Cited by 10 publications

(8 citation statements)

References 12 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Previously, an IRE motif has been predicted for distal SNCA 5′-UTR, right before the start of the SNCA ORF, but has not yet been experimentally verified [ 9 ]. For this, using nano LC-MS/MS proteomics [ 38 – 40 ], over 1300 interacting proteins were pulled down from murine brain extracts incubated with a biotin-labelled SNCA 5′-UTR RNA probe (data not shown). Tens of RBPs were identified but none matched to IRP-1 or IRP-2 and no further analysis was undertaken as a result.…”

Section: Discussionmentioning

confidence: 99%

Constitutive translation of human α-synuclein is mediated by the 5′-untranslated region

Koukouraki¹,

Doxakis²

2016

Open Biol.

View full text Add to dashboard Cite

Genetic and biochemical studies have established a central role for α-synuclein (SNCA) accumulation in the pathogenesis of Parkinson's disease. Uncovering and subsequently interfering with physiological mechanisms that control SNCA expression is one approach to limit disease progression. To this end, the long and GC-rich 5′-untranslated region (UTR) of SNCA, which is predicted to fold into stable hairpin and G-quadruplex RNA motifs, was investigated for its role in mRNA translation. Inclusion of SNCA 5′-UTR significantly induced expression of both SNCA and luciferase ORF constructs. This effect was not associated with a change in mRNA levels or differential nucleocytoplasmic shuttling. Further, the presence of the 5′-UTR enhanced SNCA synthesis when cap-dependent translation was attenuated with rapamycin treatment. Analysis using multiple methodologies revealed that the 5′-UTR harbours an internal ribosome entry site (IRES) element that spans most of its nucleotide sequence. Signals such as plasma-membrane depolarization, serum starvation and oxidative stress stimulated SNCA protein translation via its 5′-UTR as well as enhanced its IRES activity. Taken together, these data support the idea that the 5′-UTR is an important positive regulator of SNCA synthesis under diverse physiological and pathological conditions, explaining in part the abundance of SNCA in healthy neurons and its accumulation in degenerative cells.

show abstract

Section: Discussionmentioning

confidence: 99%

Constitutive translation of human α-synuclein is mediated by the 5′-untranslated region

Koukouraki¹,

Doxakis²

2016

Open Biol.

View full text Add to dashboard Cite

show abstract

“…Instead, here, we compared the features of different algorithms for peptide clustering (Table ). In addition to the approaches described herein, we considered, for feature comparison, GibbsCluster, PepServe, Hammock and UCLUST . Table provides a summary of the various features assessed in these.…”

Section: Resultsmentioning

confidence: 99%

“…In the past, several methods have been published investigating different aspects of peptide clustering, such as UCLUST, PepServe, Gibbs clustering and the Hammock algorithm . However, none of these tools provides the complete connectivity of the peptides within a cluster and a biologically meaningful consensus sequence representing each cluster, features that are of great utility, particularly in the context of immunological studies.…”

Section: Discussionmentioning

confidence: 99%

“…Several attempts have been made in the past to address this issue from different angles. For example, Hammock was developed to identify consensus motifs in large data sets, and PepServe to cluster peptides based on their physiochemical properties. Another application, UCLUST, performs rapid clustering and implements several previously identified clustering algorithms, and Andreatta et al .…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Development of a novel clustering tool for linear peptide sequences

et al. 2018

View full text Add to dashboard Cite

SummaryEpitopes identified in large‐scale screens of overlapping peptides often share significant levels of sequence identity, complicating the analysis of epitope‐related data. Clustering algorithms are often used to facilitate these analyses, but available methods are generally insufficient in their capacity to define biologically meaningful epitope clusters in the context of the immune response. To fulfil this need we developed an algorithm that generates epitope clusters based on representative or consensus sequences. This tool allows the user to cluster peptide sequences on the basis of a specified level of identity by selecting among three different method options. These include the ‘clique method’, in which all members of the cluster must share the same minimal level of identity with each other, and the ‘connected graph method’, in which all members of a cluster must share a defined level of identity with at least one other member of the cluster. In cases where it is not possible to define a clear consensus sequence with the connected graph method, a third option provides a novel ‘cluster‐breaking algorithm’ for consensus sequence driven sub‐clustering. Herein we demonstrate the tool's clustering performance and applicability using (i) a selection of dengue virus epitopes for the ‘clique method’, (ii) sets of allergen‐derived peptides from related species for the ‘connected graph method’ and (iii) large data sets of eluted ligand, major histocompatibility complex binding and T‐cell recognition data captured within the Immune Epitope Database (IEDB) with the newly developed ‘cluster‐breaking algorithm’. This novel clustering tool is accessible at http://tools.iedb.org/cluster2/.

show abstract

“…The advancement of computational tools such as databases [1][2][3][4][5], modelling [6][7][8], decision support systems [9], simu lation [10][11][12], v isualization techniques [13][14][15][16], and web servers [17][18][19][20] have revolutionized the field of bioin formatics and mo lecular biology with the breakthrough in data processing and analysis. These computational tools received wide application in various specialized disciplines in mo lecular bio logy, including systems biology [21][22], genome analysis [23][24], population genetics [25], structural bioinformatics [26][27], and phylogenetics [28][29].…”

Section: Introductionmentioning

confidence: 99%

Analysis of Tandem Repeat Patterns in Nlrc4 using a Motif Model

Tee¹

2012

IJITCS

View full text Add to dashboard Cite

Abstract-Exponential accumu lation of bio logical data requires computer scientists and bioinformat icians to improve the efficiency of co mputer algorith ms and databases. The recent advancement of computational tools has boosted the processing capacity of enormous volume of genetic data. This research applied a computational approach to analyze the tandem repeat patterns in Nlrc4 gene. Because the protein product of Nlrc4 gene is important in detecting pathogen and triggering subsequent immune responses, the results of this genetic analysis is essential for the understanding of the genetic characteristics of Nlrc4. The study on the distribution of tandem repeats may provide insights for drug design catered for the Nlrc4-imp licated diseases.

show abstract

PepServe: a web server for peptide analysis, clustering and visualization

Cited by 10 publications

References 12 publications

Constitutive translation of human α-synuclein is mediated by the 5′-untranslated region

Constitutive translation of human α-synuclein is mediated by the 5′-untranslated region

Development of a novel clustering tool for linear peptide sequences

Analysis of Tandem Repeat Patterns in Nlrc4 using a Motif Model

Contact Info

Product

Resources

About