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Literature DB >> 28039164

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

Alex V Kochetov^1,2, Jens Allmer³, Alexandra I Klimenko¹, Bulat S Zuraev^1,2, Yury G Matushkin¹, Sergey A Lashin^1,2.

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.

Mesh：

Substances：
RNA, Messenger

Year: 2017 PMID： 28039164 DOI： 10.1093/bioinformatics/btw736

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

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Cited

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Journal: PLoS Comput Biol Date: 2019-02-08 Impact factor: 4.475

Review 2. Best practices for bioinformatic characterization of neoantigens for clinical utility.

Authors: Megan M Richters; Huiming Xia; Katie M Campbell; William E Gillanders; Obi L Griffith; Malachi Griffith
Journal: Genome Med Date: 2019-08-28 Impact factor: 11.117

3. The mTOR Signaling Pathway Activity and Vitamin D Availability Control the Expression of Most Autism Predisposition Genes.

Authors: Ekaterina A Trifonova; Alexandra I Klimenko; Zakhar S Mustafin; Sergey A Lashin; Alex V Kochetov
Journal: Int J Mol Sci Date: 2019-12-15 Impact factor: 5.923

7. Premature Termination Codon in 5' Region of Desmoplakin and Plakoglobin Genes May Escape Nonsense-Mediated Decay through the Reinitiation of Translation.

Authors: Marta Vallverdú-Prats; Ramon Brugada; Mireia Alcalde
Journal: Int J Mol Sci Date: 2022-01-07 Impact factor: 5.923

7 in total

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

1. BioJava 5: A community driven open-source bioinformatics library.

Review 2. Best practices for bioinformatic characterization of neoantigens for clinical utility.

3. The mTOR Signaling Pathway Activity and Vitamin D Availability Control the Expression of Most Autism Predisposition Genes.

4. Tandem repeats ubiquitously flank and contribute to translation initiation sites.

5. riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data.

6. Link between short tandem repeats and translation initiation site selection.

7. Premature Termination Codon in 5' Region of Desmoplakin and Plakoglobin Genes May Escape Nonsense-Mediated Decay through the Reinitiation of Translation.