About: LAMPA, LArge Multidomain Protein Annotator, and its application to RNA virus polyproteins

Facets (new session)
Description
Metadata
Settings
- owl:sameAs
- Inference Rule:

About: LAMPA, LArge Multidomain Protein Annotator, and its application to RNA virus polyproteins Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	LAMPA, LArge Multidomain Protein Annotator, and its application to RNA virus polyproteins
Creator	Gulyaeva, Anastasia Samborskiy, Dmitry Gorbalenya, Alexander Ocheredko, Elena Sigorskih, Andrey
Source	Medline; PMC
abstract	MOTIVATION: To facilitate accurate estimation of statistical significance of sequence similarity in profile–profile searches, queries should ideally correspond to protein domains. For multidomain proteins, using domains as queries depends on delineation of domain borders, which may be unknown. Thus, proteins are commonly used as queries that complicate establishing homology for similarities close to cutoff levels of statistical significance. RESULTS: In this article, we describe an iterative approach, called LAMPA, LArge Multidomain Protein Annotator, that resolves the above conundrum by gradual expansion of hit coverage of multidomain proteins through re-evaluating statistical significance of hit similarity using ever smaller queries defined at each iteration. LAMPA employs TMHMM and HHsearch for recognition of transmembrane regions and homology, respectively. We used Pfam database for annotating 2985 multidomain proteins (polyproteins) composed of >1000 amino acid residues, which dominate proteomes of RNA viruses. Under strict cutoffs, LAMPA outperformed HHsearch-mediated runs using intact polyproteins as queries by three measures: number of and coverage by identified homologous regions, and number of hit Pfam profiles. Compared to HHsearch, LAMPA identified 507 extra homologous regions in 14.4% of polyproteins. This Pfam-based annotation of RNA virus polyproteins by LAMPA was also superior to RefSeq expert annotation by two measures, region number and annotated length, for 69.3% of RNA virus polyprotein entries. We rationalized the obtained results based on dependencies of HHsearch hit statistical significance for local alignment similarity score from lengths and diversities of query-target pairs in computational experiments. AVAILABILITY AND IMPLEMENTATION: LAMPA 1.0.0 R package is placed at github (https://github.com/Gorbalenya-Lab/LAMPA). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
has issue date	2020-05-01(xsd:dateTime)
bibo:doi	10.1093/bioinformatics/btaa065
bibo:pmid	32003788
has license	cc-by-nc
sha1sum (hex)	bfb040be783e4dfa1bf6e73de44dec2f1a013fdc
schema:url	https://doi.org/10.1093/bioinformatics/btaa065
resource representing a document's title	LAMPA, LArge Multidomain Protein Annotator, and its application to RNA virus polyproteins
has PubMed Central identifier	PMC7203729
has PubMed identifier	32003788
schema:publication	Bioinformatics
resource representing a document's body	covid:bfb040be783e4dfa1bf6e73de44dec2f1a013fdc#body_text
is schema:about of	named entity 'composed' named entity 'Protein' named entity 'pairs' named entity 'homologous regions' named entity 'statistical significance' named entity 'homology' named entity 'statistical significance' named entity 'Sequence analysis' named entity 'polyproteins' named entity 'extra' named entity 'statistical significance' named entity 'polyproteins' named entity 'amino acid' named entity 'polyproteins' named entity 'levels' named entity 'resolves' named entity 'RNA virus' named entity 'coverage' named entity 'acid' named entity 'region' named entity 'iterative' named entity 'based' named entity 'For' named entity 'application' named entity 'statistical significance' named entity 'Pfam' named entity 'database' named entity 'Multidomain Protein' named entity 'statistical significance' named entity 'HHsearch' named entity 'RNA virus' named entity 'HHsearch' named entity 'RNA virus' named entity 'Sequence analysis' named entity 'LAMPA' named entity 'multidomain proteins' named entity 'Secondary structures' named entity 'Jupyter notebook' named entity 'database' named entity 'R package' named entity 'homology' named entity 'P-value' named entity 'HHsearch' named entity 'HHsearch' named entity 'Pfam' named entity 'post-processing' named entity 'statistical significance' named entity 'structural domain' named entity 'HHsearch' named entity 'Wilcoxon signed-rank test' named entity 'Pfam' named entity 'Probabilities' named entity '68.2%' named entity 'linear dependence' named entity 'HHsearch' named entity 'sequence identity' named entity 'helix' named entity 'Probability' named entity '2.2' named entity 'Probability' named entity 'false positives' named entity 'Probability' named entity 'multidomain proteins' named entity '95%' named entity 'ssRNA' named entity 'multidomain proteins' named entity 'multidomain proteins' named entity 'RefSeq' named entity 'HHsearch' named entity 'Probability' named entity 'PSIPRED' named entity 'severe acute respiratory syndrome' named entity '95%' named entity 'Probability' named entity 'bioinformatics' named entity 'RNA virus' named entity 'neural networks'

Faceted Search & Find service v1.13.91 as of Mar 24 2020

Alternative Linked Data Documents: Sponger | ODE Content Formats:

RDF

ODATA

Microdata

About

OpenLink Virtuoso version 07.20.3229 as of Jul 10 2020, on Linux (x86_64-pc-linux-gnu), Single-Server Edition (94 GB total memory)
Data on this page belongs to its respective rights holders.
Virtuoso Faceted Browser Copyright © 2009-2025 OpenLink Software