Zur Kurzanzeige

2021-06-14Zeitschriftenartikel
smORFer: a modular algorithm to detect small ORFs in prokaryotes
dc.contributor.authorBartholomäus, Alexander
dc.contributor.authorKolte, Baban
dc.contributor.authorMustafayeva, Ayten
dc.contributor.authorGoebel, Ingrid
dc.contributor.authorFuchs, Stephan
dc.contributor.authorBenndorf, Dirk
dc.contributor.authorEngelmann, Susanne
dc.contributor.authorIgnatova, Zoya
dc.date.accessioned2024-07-26T14:46:07Z
dc.date.available2024-07-26T14:46:07Z
dc.date.issued2021-06-14none
dc.identifier.other10.1093/nar/gkab477
dc.identifier.urihttp://edoc.rki.de/176904/11867
dc.description.abstractEmerging evidence places small proteins (≤50 amino acids) more centrally in physiological processes. Yet, their functional identification and the systematic genome annotation of their cognate small open-reading frames (smORFs) remains challenging both experimentally and computationally. Ribosome profiling or Ribo-Seq (that is a deep sequencing of ribosome-protected fragments) enables detecting of actively translated open-reading frames (ORFs) and empirical annotation of coding sequences (CDSs) using the in-register translation pattern that is characteristic for genuinely translating ribosomes. Multiple identifiers of ORFs that use the 3-nt periodicity in Ribo-Seq data sets have been successful in eukaryotic smORF annotation. They have difficulties evaluating prokaryotic genomes due to the unique architecture (e.g. polycistronic messages, overlapping ORFs, leaderless translation, non-canonical initiation etc.). Here, we present a new algorithm, smORFer, which performs with high accuracy in prokaryotic organisms in detecting putative smORFs. The unique feature of smORFer is that it uses an integrated approach and considers structural features of the genetic sequence along with in-frame translation and uses Fourier transform to convert these parameters into a measurable score to faithfully select smORFs. The algorithm is executed in a modular way, and dependent on the data available for a particular organism, different modules can be selected for smORF search.eng
dc.language.isoengnone
dc.publisherRobert Koch-Institut
dc.rights(CC BY 3.0 DE) Namensnennung 3.0 Deutschlandger
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/de/
dc.subjectcomputational methodseng
dc.subjectribosomes and protein translationeng
dc.subjectgenomicseng
dc.subject.ddc610 Medizin und Gesundheitnone
dc.titlesmORFer: a modular algorithm to detect small ORFs in prokaryotesnone
dc.typearticle
dc.identifier.urnurn:nbn:de:0257-176904/11867-5
dc.type.versionpublishedVersionnone
local.edoc.container-titleNucleic Acid Researchnone
local.edoc.container-issn1362-4962none
local.edoc.pages12none
local.edoc.type-nameZeitschriftenartikel
local.edoc.container-typeperiodical
local.edoc.container-type-nameZeitschrift
local.edoc.container-urlhttps://academic.oup.com/narnone
local.edoc.container-publisher-nameOxford University Pressnone
local.edoc.container-volume49none
local.edoc.container-issue15none
local.edoc.container-reportyear2021none
dc.description.versionPeer Reviewednone

Zur Kurzanzeige