AltORFev有助于预测真核生物mRNA中的可变开放阅读框。

AltORFev facilitates the prediction of alternative open reading frames in eukaryotic mRNAs.

作者信息

Kochetov Alex V, Allmer Jens, Klimenko Alexandra I, Zuraev Bulat S, Matushkin Yury G, Lashin Sergey A

机构信息

Institute of Cytology & Genetics, SB RAS, Novosibirsk, Russia.

Novosibirsk State University, Novosibirsk, Russia.

出版信息

Bioinformatics. 2017 Mar 15;33(6):923-925. doi: 10.1093/bioinformatics/btw736.

DOI:10.1093/bioinformatics/btw736

PMID:28039164

Abstract

MOTIVATION

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.

AVAILABILITY AND IMPLEMENTATION

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.

CONTACT

ak@bionet.nsc.ru.

摘要

动机

蛋白质合成并非一个简单直接的过程，一个基因位点可以产生多种异构体，例如，通过从不同的起始位点开始mRNA翻译。altORF评估器（altORFev）预测真核生物mRNA中通过线性扫描机制及其修饰（渗漏扫描和重新起始）翻译的可变开放阅读框。该程序揭示了大多数落在mRNA 5'端的40S核糖体亚基识别的有效翻译的可变开放阅读框。这些信息有助于揭示与注释蛋白质的未知异构体或新的无关多肽合成相关的真核基因的功能。