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ORFipy (version 0.0.4+galaxy1)

Find ORFs in::

ORFs will be detected in this sequence

Specify genetic code:

Select outputs:

DNA, RNA, and Peptide options will produce FASTA outputs

Select strand:

Identify ORFs on which strand

Minimum length of ORFs:

No ORFs below this value will be reported. All ORFs will be reported if this parameter is not set. Default is 30

Maximum length of ORFs:

This value doesn't take in account the STOP codon. No ORFs over this value will be reported. Default is 1.000.000.000.

Start codon(s) to use:

A comma-separated list without spaces. Only ATCG and comma are allowed

Stop codon(s) to use:

A commma separated list without spaces. Only ATCG and comma are allowed

Ignore case?:

Ignore case and find ORFs in lower case sequences too. NO = do not ignore (use upper case only). YES = ignore

Output ORFs with Start but no Stop?:

Output ORFs with a start codon but lacking an inframe stop codon. NO = do not output. YES = do output

Output ORFs with Stop but no Start?:

Output ORFs with an inframe stop codon lacking an inframe start codon. NO = do not output. YES = do output

Output ORFs bound by Stop codons?:

Output ORFs defined as regions between stop codons (regions free of stop codon). This will set --partial-3 and --partial-5 true

Include stop codon in the results?:

Output ORFs with an inframe stop codon lacking an inframe start codon. NO = do not include. YES = include

What it does

Orfipy is a tool for finding open reading frames (ORFs).

Parameters

Galaxy interface of Orfipy supports the following parameters (the following is taken from the tool help):

--table TABLE The codon table number to use or path to .json file
with codon table. Use --show-tables to see available
tables compiled from: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?chapter=cgencodes Default: 1
--start START Comma-separated list of start-codons. This will
override start codons described in translation table.
E.g. "--start ATG,ATT" Default: Derived from the
translation table selected
--stop STOP Comma-separated list of stop codons. This will
override stop codons described in translation table.
E.g. "--start TAG,TTT" Default: Derived from the
translation table selected
--outdir OUTDIR Path to outdir default: orfipy_<infasta>_out
--bed12 BED12 bed12 out file Default: None
--bed BED bed out file Default: None
--dna DNA fasta (DNA) out file Default: None
--rna RNA fasta (RNA) out file Default: None
--pep PEP fasta (peptide) out file Default: None
--min MIN Minimum length of ORF, excluding stop codon
(nucleotide) Default: 30
--max MAX Maximum length of ORF, excluding stop codon
(nucleotide) Default: 1,000,000,000
--strand {f,r,b} Strands to find ORFs [(f)orward,(r)everse,(b)oth]
Default: b
--ignore-case Ignore case and find ORFs in lower case sequences too.
Useful for soft-masked sequences. Default: False
--partial-3 Output ORFs with a start codon but lacking an inframe
stop codon. E.g. "ATG TTT AAA" Default: False
--partial-5 Output ORFs with an inframe stop codon lacking an
inframe start codon. E.g. "TTT AAA TAG" Default: False
--between-stops Output ORFs defined as regions between stop codons
(regions free of stop codon). This will set
--partial-3 and --partial-5 true. Default: False
--include-stop Include stop codon in the results, if a stop codon
exists. This output format is compatible with
TransDecoder's which includes stop codon coordinates
Default: False