OrfPredictor statistics

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Citations per year

Number of citations per year for the bioinformatics software tool OrfPredictor
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Tool usage distribution map

This map represents all the scientific publications referring to OrfPredictor per scientific context
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Protocols

OrfPredictor specifications

Information


Unique identifier OMICS_10603
Name OrfPredictor
Interface Web user interface
Restrictions to use None
Input data Sequences
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Xiang Jia Min

Publication for OrfPredictor

OrfPredictor citations

 (93)
library_books

Analysis of Homologs of Cry toxin Receptor Related Proteins in the Midgut of a Non Bt Target, Nilaparvata lugens (Stål) (Hemiptera: Delphacidae)

2018
PMCID: 5804751
PMID: 29415259
DOI: 10.1093/jisesa/iex102

[…] The OrfPredictor program () was used to obtain the open reading frame (ORF) of each unigene. Three ORF predictions were made for nucleotide sequence of each unigene, starting from the first, the second, a […]

library_books

Elucidating the Small Regulatory RNA Repertoire of the Sea Anemone Anemonia viridis Based on Whole Genome and Small RNA Sequencing

2018
Genome Biol Evol
PMCID: 5793845
PMID: 29385567
DOI: 10.1093/gbe/evy003

[…] or to the small RNA alignment. Genomic setting of aligned putative miRNAs was inspected for overlapping regions corresponding to open reading frames (ORFs). Our scaffolds were searched for ORFs using OrfPredictor (http://bioinformatics.ysu.edu/tools/OrfPredictor.html; last accessed January 14, 2018) (). […]

library_books

Species specific genes under selection characterize the co evolution of slavemaker and host lifestyles

2017
BMC Evol Biol
PMCID: 5715652
PMID: 29202686
DOI: 10.1186/s12862-017-1078-9

[…] workbench (Qiagen) and MIRA [] (Additional file ; for more details see []). Contigs were annotated using BlastX v.2.2.30 against the non-redundant arthropod database (November 2014). The online tool ORFpredictor 2.0.3 [] was used to predict open reading frames and amino acid sequences for all contigs. The predicted and translated amino acid sequences were used as input for OrthoMCL 2.0.9 [], to b […]

call_split

Highly Expressed Genes Are Preferentially Co Opted for C4 Photosynthesis

2017
Mol Biol Evol
PMCID: 5850498
PMID: 29040657
DOI: 10.1093/molbev/msx269
call_split See protocol

[…] CDSs were predicted from the assembled contigs and those retrieved from the literature using the standalone version of OrfPredictor (). Protein sequences of eight publicly available genomes (Arabidopsis thaliana, Brachypodium distachyon, Glycine max, Oryza sativa, Populus trichocarpa, S. italica, So. bicolor, and Z. m […]

library_books

A new method for sequencing the hypervariable Plasmodium falciparum gene var2csa from clinical samples

2017
Malar J
PMCID: 5561619
PMID: 28818101
DOI: 10.1186/s12936-017-1976-8

[…] lysis. This 100× threshold was chosen because this was the minimum depth of coverage at which a perfect consensus sequence of the reference 3D7 was obtained. Then the amplicon sequences were fed into OrfPredictor [] to predict open reading frames, and corresponding amino acid sequences were generated. Amino acid sequences were used to annotate constituent domains using the VarDom 1.0 server []. Mu […]

call_split

First Complete Genome Sequence of Tobacco necrosis virus D Isolated from Soybean and from North America

2017
Genome Announc
PMCID: 5552992
PMID: 28798183
DOI: 10.1128/genomeA.00781-17
call_split See protocol

[…] f 812×. The overall genome sequence identities between TNV-DMB and the other TNV-D isolates were 83.4% (TNV-D), 93.3% (TNV-DH), and 83.2% (TNV-DP). Gene prediction using FgenesV (Softberry, Inc.) and OrfPredictor () identified the same six protein coding genes found in the other sequenced isolates in the following order: 22-kDa and 82-kDa genes encoding products required for RNA replication (p22 a […]


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OrfPredictor institution(s)
Centre for Structural and Functional Genomics, Concordia University Montreal, QC, Canada
OrfPredictor funding source(s)
This project was supported by Genome Quebec and Genome Canada.

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