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Open reading frame detection software tools | Shotgun metagenomic sequencing data analysis

Finding and translating stretches of DNA lacking stop codons is a task common in the analysis of sequence data. However the computational tools for finding open reading frames are sufficiently slow that they are becoming a bottleneck as the volume…
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getorf
Web

getorf

Finds and extracts open reading frames (ORFs). An ORF may be defined as a…

Finds and extracts open reading frames (ORFs). An ORF may be defined as a region of a specified minimum size between two STOP codons, or between a START and a STOP codon.

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OrfM
Desktop

OrfM

Rapidly identifies open reading frames (ORFs) in sequence data by applying the…

Rapidly identifies open reading frames (ORFs) in sequence data by applying the Aho-Corasick algorithm to find regions uninterrupted by stop codons. Benchmarking revealed that OrfM finds identical…

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ORF search &…
Web

ORF search & Translator

Assists user in translation of DNA sequences.

Assists user in translation of DNA sequences.

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Open Reading…
Web
Desktop

Open Reading Frame Finder

Searches open reading frames (ORFs) in the DNA sequence. Open Reading Frame…

Searches open reading frames (ORFs) in the DNA sequence. Open Reading Frame Finder returns the range of each ORF, along with its protein translation. It uses ORF finder to search newly sequenced DNA…

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plotorf
Desktop

plotorf

Plots potential open reading frames (ORFs) for an input nucleotide sequence.…

Plots potential open reading frames (ORFs) for an input nucleotide sequence. plotorf is only really useful when dealing with prokaryotic or mRNA eukaryotic sequences. ORFs in this program are defined…

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sixpack
Desktop

sixpack

Displays a DNA sequence with 6-frame translation and open reading frames…

Displays a DNA sequence with 6-frame translation and open reading frames (ORFs). sixpack reads a DNA sequence and writes an output file giving out the forward and reverse sense sequences with the…

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checktrans
Desktop

checktrans

Reports STOP codons and open reading frame (ORFs) statistics of a protein.…

Reports STOP codons and open reading frame (ORFs) statistics of a protein. checktrans reads a protein sequence containing stop characters and writes a statistical report of any ORFs that are greater…

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sORF finder
Web
Desktop

sORF finder Small Open Reading Frames

Serves to identify small open reading frames (sORFs) with 10 to 100 amino acids…

Serves to identify small open reading frames (sORFs) with 10 to 100 amino acids and with high-coding potential in all six frames of a given nucleotide sequence. SORF finder works with a set of 5…

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AntiFam
Dataset

AntiFam

Offers a collection of multiple sequence alignments and profiles hidden Markov…

Offers a collection of multiple sequence alignments and profiles hidden Markov models (HMMs). AntiFam can assist to identify spurious open reading frames (ORFs) in protein annotation. It can be used…

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