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Repository get_orfs_or_cdss

Name: get_orfs_or_cdss

Owner: peterjc

Synopsis: Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)

Detailed description:

This tool is a short Python script (using Biopython library functions) to search
nucleotide sequences for open reading frames (ORFs) or coding sequences (CDSs) where
the first potential start codon is used.

It is intended for very simplistic gene finding in Prokaryotes and viruses, or for
finding the likely CDS in an EST or mRNA sequence. It is not suitable for Eurakoytic
gene prediction since it is not intro aware.

See also the EMBOSS tool ``getorf`` which also has a Galaxy wrapper. This offers
much of the same functionality, but is likely faster as it is written in C.

Content homepage: https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss

Development repository: https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss

Link to this repository: https://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/eaf1d40eceb4

Clone this repository: hg clone https://testtoolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss

Type: unrestricted

Revision: 31:eaf1d40eceb4

This revision can be installed: True

Times cloned / installed: 649

Tool dependencies - repository tools require handling of these dependencies
Name	Version	Type
biopython	1.67	package

Tool dependencies - repository tools require handling of these dependencies

Name

Version

Type

biopython

1.67

package

Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
Name	Description	Version	Minimum Galaxy Version
Get open reading frames (ORFs) or coding sequences (CDSs) View tool metadata	e.g. to get peptides from ESTs	0.2.3	16.01

Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata

Name

Description

Version

Minimum Galaxy Version

View tool metadata

e.g. to get peptides from ESTs

0.2.3

16.01