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Protocols

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 citations

 (824)
call_split

The bipartite mitochondrial genome of Ruizia karukerae (Rhigonematomorpha, Nematoda)

2018
Sci Rep
PMCID: 5945635
PMID: 29749383
DOI: 10.1038/s41598-018-25759-0
call_split See protocol

[…] The 12 mitochondrial protein-coding genes and two ribosomal RNA genes of R. karukerae were identified using the annotation program DOGMA and ORF finder (NCBI), and were confirmed by comparing nucleotide sequences with those from closely related nematodes. Putative secondary structures of 22 tRNA genes were inferred using the program tRNAsc […]

call_split

Comparative analyses of the complete mitochondrial genomes of Dosinia clams and their phylogenetic position within Veneridae

2018
PLoS One
PMCID: 5931646
PMID: 29718949
DOI: 10.1371/journal.pone.0196466
call_split See protocol

[…] by sequencing the PCR-amplified DNA fragments were analyzed and assembled using Seqman program from DNASTAR (available at: http://www.dnastar.com/). Protein coding genes were annotated by using NCBI ORF Finder (https://www.ncbi.nlm.nih.gov/orffinder/) and BLASTx with the invertebrate mitochondrial code. The positions of tRNA genes were determined by ARWEN v.1.2 [] and MITOS Web Server []; and sec […]

call_split

Complete Genomic Analysis of a Salmonella enterica Serovar Typhimurium Isolate Cultured From Ready to Eat Pork in China Carrying One Large Plasmid Containing mcr 1

2018
Front Microbiol
PMCID: 5934421
PMID: 29755416
DOI: 10.3389/fmicb.2018.00616
call_split See protocol

[…] SMRT® Pacific Biosciences RS II platform (Pacific Biosciences, Menlo Park, CA, United States). Annotation of the genomes was performed using RAST, BLASTn and BLASTp programs. The open reading frame (ORF) Finder program was used to identify features of public health interest. PlasmidFinder-1.3 was used to identify plasmid replicon types. The comprehensive antibiotic resistance database (CARD) was […]

library_books

Pheromone Binding Protein EhipPBP1 Is Highly Enriched in the Male Antennae of the Seabuckthorn Carpenterworm and Is Binding to Sex Pheromone Components

2018
Front Physiol
PMCID: 5934486
PMID: 29755369
DOI: 10.3389/fphys.2018.00447

[…] 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 of E […]

call_split

Transcription Factor SmWRKY1 Positively Promotes the Biosynthesis of Tanshinones in Salvia miltiorrhiza

2018
Front Plant Sci
PMCID: 5934499
PMID: 29755494
DOI: 10.3389/fpls.2018.00554
call_split See protocol

[…] s used for identification of SmWRKY1 were listed in Supplementary Table . The characteristics of SmWRKY1 were further analyzed by a series of bioinformatics tools. Nucleotide blast, protein blast and ORF Finder were used to analyze nucleotide sequence and the complete open reading frame. MEGA 6 was applied to construct a phylogenetic tree by the neighbor-joining (NJ) method and 1000 replications w […]

library_books

Identification and characterization of a plastidial ω 3 fatty acid desaturase EgFAD8 from oil palm (Elaeis guineensis Jacq.) and its promoter response to light and low temperature

2018
PLoS One
PMCID: 5919639
PMID: 29698515
DOI: 10.1371/journal.pone.0196693

[…] Nucleotide and amino acid sequence analyses used the BLAST program and open reading frame (ORF) finder from NCBI website (https://www.ncbi.nlm.nih.gov/). Amino acid alignment of fatty acid desaturases was performed by ClustalX 2.1 program with default setting []. A phylogenetic tree was con […]


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