Open Reading Frame Finder protocols

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Open Reading Frame Finder specifications

Information


Unique identifier OMICS_17682
Name Open Reading Frame Finder
Alternative names CDS Finder, ORF Finder
Interface Web user interface
Restrictions to use None
Input data Accession number, gi, or nucleotide sequence.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Information


Unique identifier OMICS_17682
Name Open Reading Frame Finder
Alternative names CDS Finder, ORF Finder
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Open Reading Frame Finder in pipelines

 (21)
2018
PMCID: 5952423
PMID: 29764461
DOI: 10.1186/s12985-018-0998-3

[…] from overnight cultures were sequenced (mclab, san francisco, ca)., the sequences were assembled and analyzed by the clc genomics workbench. open reading frames (orfs) were predicted using the open reading frame finder at https://www.ncbi.nlm.nih.gov/orffinder/. multiple alignments of genomic sequences and deduced amino acid sequences of individual viral genes were performed […]

2017
PMCID: 5397871
PMID: 28425468
DOI: 10.1038/srep46163

[…] cuticle biosynthesis, transport and regulation were obtained from our mango database using blastx (e-value ≤ 1e-5). the coding dna sequence (cds) and deduced amino acid sequence were obtained using open reading frame finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html). signal-3l was used to identify signal peptides and predgpi predictor to identify glycosylphosphatidylinositol (gpi) domains. […]

2017
PMCID: 5447745
PMID: 28611814
DOI: 10.3389/fpls.2017.00902

[…] ncbi database and the cucurbitaceae database of the weng lab at the university of wisconsin-madison, madison, wi, united states, using softberry to predict candidate gene structures and using the open reading frame finder fgenesh. multiple nuclear sequence alignment was used dnaman6.0 software., the segregation distribution of male sterility among test materials in 2 years, spring 2014 […]

2017
PMCID: 5506516
PMID: 28455670
DOI: 10.1007/s00705-017-3383-4

[…] with a sequence run-off experiment and comparison of the nucleotide sequence with the ligated phage ends., three bioinformatic on-line programs were used for orfs prediction in the ϕ16 genome: open reading frame finder (https://www.ncbi.nlm.nih.gov/orffinder/), glimmer 3 (http://www.ncbi.nlm.nih.gov/genomes/microbes/glimmer_3.cgi) and genemark s (http://exon.biology.gatech.edu/). […]

2017
PMCID: 5557890
PMID: 28811654
DOI: 10.1038/s41598-017-08566-x

[…] gel extraction kit (omega, usa) and cloned into the pmd19-t vector (takara, japan) and the recombinant vectors were transformed into trans1-t1 competent cells (transgen, china) and sequenced., open reading frame finder (http://www.ncbi.nlm.nih.gov/gorf/orfig.cgi) was used to analyse cdna sequences and deduce the corresponding polypeptides they encode. smart (simple modular architecture […]


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Open Reading Frame Finder in publications

 (67)
PMCID: 5934486
PMID: 29755369
DOI: 10.3389/fphys.2018.00447

[…] ampicillin). colony pcr was used to select positive clones and the amplified dna was then sequenced (qingke, beijing, china)., from the coding sequence of ehippbp1, the orfs were deduced using the open reading frame finder. putative signal peptides were predicted using the signalp 4.1 server (). the molecular weights of the proteins were predicted using swiss-prot. three-dimensional models […]

PMCID: 5744146
PMID: 29207524
DOI: 10.3390/v9120371

[…] workbench 7.5.1 software (clc bio, aarhus, denmark). reads were analyzed with default settings, except for trimming (q-score: >20; read length: >300 bp). the orfs were searched using an open reading frame finder (http://www.ncbi.nlm.nih.gov/orffinder/) and then homologues were analyzed using a blast search., maximum-likelihood phylogenetic trees were constructed using mega 6.0 […]

PMCID: 5664376
PMID: 29181384
DOI: 10.1155/2017/2763259

[…] untranslated regions (utrs), and poly-a tail regions were located by softberry server (http://www.softberry.com/berry.phtml). the conceptual translation of nucleotide sequence was done by using the open reading frame finder (orf) program (http://www.ncbi.nlm.nih.gov/gorf/gorf.html). molecular weight and subcellular localization were carried out at expasy server (http://expasy.org). psipred […]

PMCID: 5637498
PMID: 29025938
DOI: 10.1128/genomeA.01046-17

[…] surfactin, bacillibactin, and bacilysin (). locillomycin is produced by bacillus subtilis ()., the lantibiotic gene cluster in contig 19 was analyzed via the national center for biotechnology open reading frame finder (). the open reading frames necessary for the production of a two-component lantibiotic were identified. the gene cluster included those for amyloliquecidin gf610 alpha […]

PMCID: 5622057
PMID: 28963554
DOI: 10.1038/s41598-017-12646-3

[…] were described as previously.table 1 , the cck cdna and deduced amino acid sequences were analyzed by employing blastn and blastp (http://www.ncbi.nlm.nih.gov). the cck orf was predicted with the open reading frame finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html). besides, the cleavage site of the signal peptide was predicted by using signalp 4.1 server […]


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