Open Reading Frame Finder pipeline

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

 (7)
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 […]

2015
PMCID: 4414451
PMID: 25923714
DOI: 10.1371/journal.pone.0125242

[…] blast results or with high homology to one another were eliminated selectively as allelic variants or as different parts of the same gene [26]. the complete coding region was determined using the open reading frame finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html), and protein blast results were generated. genes of other species were downloaded from the ncbi database and used as references. […]

2014
PMCID: 4105107
PMID: 25015379
DOI: 10.1186/1756-3305-7-319

[…] the complete mt genome sequences of other nematodes (available in genbank) using the computer program mafft 7 [28] to infer gene boundaries. the open-reading frames (orfs) were predicted by the open reading frame finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html) using the invertebrate mitochondrial code and subsequently compared with those of trichostrongylus axei and trichostrongylus […]

2014
PMCID: 4433956
PMID: 26019489
DOI: 10.1080/13102818.2014.901665

[…] and vector sequences were trimmed. in all the sequenced its regions, after vector trimming open reading frames (orfs) were predicted using the national center for biotechnology information (ncbi) open reading frame finder (http://www.ncbi.nlm.nih.gov/gorf/gorf). the trimmed sequences were further aligned using muscle v3.70+ fix1-2 [25] and the resulting alignments were manually checked. gaps […]

2012
PMCID: 3563745
PMID: 28324349
DOI: 10.1007/s13205-012-0065-5

[…] in another study, the isolation and identification of a novel esterase from a bac library clone with an insert size of 5.1 kb derived from yangtze river in china was reported (wu and sun 2009). open reading frame finder analysis of that insert after sequencing indicated the presence of three orfs, each >900 bp. one of the three orfs was confirmed to encode an esterase (1,479–2,747 bp) […]

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