ORFipy

 a versatile ORF finder (Galaxy Version 0.0.4+galaxy2)

Tool Parameters

Please provide a value for this option.
* required
ORFs will be detected in this sequence
*
(--table)
- optional
DNA, RNA, and Peptide options will produce FASTA outputs
*
Identify ORFs on which strand (--strand)
- optional
No ORFs below this value will be reported. All ORFs will be reported if this parameter is not set. Default is 30 (--min)
- optional
This value doesn't take in account the STOP codon. No ORFs over this value will be reported. Default is 1.000.000.000. (--max)
- optional
A comma-separated list without spaces. Only ATCG and comma are allowed (--start)
- optional
A commma separated list without spaces. Only ATCG and comma are allowed (--stop)
Ignore case and find ORFs in lower case sequences too. NO = do not ignore (use upper case only). YES = ignore (--ignore-case)
Output ORFs with a start codon but lacking an inframe stop codon. NO = do not output. YES = do output (--partial-3)
Output ORFs with an inframe stop codon lacking an inframe start codon. NO = do not output. YES = do output (--partial-5)
Output ORFs defined as regions between stop codons (regions free of stop codon). This will set --partial-3 and --partial-5 true (--between-stops)
Output ORFs with an inframe stop codon lacking an inframe start codon. NO = do not include. YES = include (--include-stop)
Setting this option will automatically enable the BED option. (--longest)

Additional Options

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Help

What it does

Orfipy is a tool for finding open reading frames (ORFs) in sequences (FASTA files).

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Citations
Requirements See details
- orfipy (Version 0.0.4)
References

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