title: AltORFev facilitates the prediction of alternative open reading frames in eukaryotic mRNAs.
abstract: Protein synthesis is not a straight forward process and one gene locus can produce many isoforms, for example, by starting mRNA translation from alternative start sites. altORF evaluator (altORFev) predicts alternative open reading frames within eukaryotic mRNA translated by a linear scanning mechanism and its modifications (leaky scanning and reinitiation). The program reveals the efficiently translated altORFs recognized by the majority of 40S ribosomal subunits landing on the 5'-end of an mRNA. This information aids to reveal the functions of eukaryotic genes connected to synthesis of either unknown isoforms of annotated proteins or new unrelated polypeptides.
  
  
  
  altORFev is available at http://www.bionet.nsc.ru/AUGWeb/ and has been developed in Java 1.8 using the BioJava library; and the Vaadin framework to produce the web service.
  
  
  
  ak@bionet.nsc.ru.
authors.affiliation: Institute of Cytology & Genetics, SB RAS, Novosibirsk, Russia.|Novosibirsk State University, Novosibirsk, Russia.
authors.forename: Alex V
authors.initials: AV
authors.lastname: Kochetov
authors.affiliation: Molecular Biology and Genetics, Izmir Institute of Technologies, Izmir, Turkey.
authors.forename: Jens
authors.initials: J
authors.lastname: Allmer
authors.affiliation: Institute of Cytology & Genetics, SB RAS, Novosibirsk, Russia.
authors.forename: Alexandra I
authors.initials: AI
authors.lastname: Klimenko
authors.affiliation: Institute of Cytology & Genetics, SB RAS, Novosibirsk, Russia.|Novosibirsk State University, Novosibirsk, Russia.
authors.forename: Bulat S
authors.initials: BS
authors.lastname: Zuraev
authors.affiliation: Institute of Cytology & Genetics, SB RAS, Novosibirsk, Russia.
authors.forename: Yury G
authors.initials: YG
authors.lastname: Matushkin
authors.affiliation: Institute of Cytology & Genetics, SB RAS, Novosibirsk, Russia.|Novosibirsk State University, Novosibirsk, Russia.
authors.forename: Sergey A
authors.initials: SA
authors.lastname: Lashin
mesh_terms: D056890:Eukaryota / Q000235:genetics; D023281:Genomics / Q000379:methods*; D016366:Open Reading Frames; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000378:metabolism*; D054682:Ribosome Subunits, Small, Eukaryotic / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods; D012984:Software
chemical_list: D012333:RNA, Messenger