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2024年6月18日发(作者：)

*** Input query options (one of them has to be provided):

-in

name of file with the nucleotide sequence in FASTA format

(more than one sequence is allowed)

Default = `'

-id

Accession or gi number of the nucleotide sequence

(ignored, if the file name is provided)

Default = `'

*** Query sequence details:

-b

Start address of sequence fragment to be processed

Default = `1'

-e

Stop address of sequence fragment to be processed (0 - to the end of the

sequence)

Default = `0'

-c

Is the sequence circular? (t/f) *** Under development

Default = `false'

*** Search parameters:

-g

Genetic code to use (1-31)

see /Taxonomy/Utils/ for details

Default = `1'

-s

ORF start codon to use:

0 = "ATG" only

1 = "ATG" and alternative initiation codons

2 = any sense codon

Default = `1'

-ml

Minimal length of the ORF (nt)

Value less than 30 is automatically changed by 30.

Default = `75'

-n

Ignore nested ORFs (completely placed within another)

Default = `false'

-strand

Output ORFs on specified strand only (both|plus|minus)

Default = `both'

*** Output options:

-out

Output file name

-outfmt

Output options:

0 = list of ORFs in FASTA format

1 = CDS in FASTA format

2 = Text ASN.1

3 = Feature table

Default = `0'

　　

ORFfinder -in -s 2 -ml 100 -out -outfmt 3

　　

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