Module Detail Information

Name:Getorf
Type: Module
Short URL:
http://bit.ly/1B7EckL
Description:This program finds and outputs the sequences of open reading frames (ORFs). The ORFs can be defined as regions of a specified minimum size between STOP codons or between START and STOP codons. The ORFs can be output as the nucleotide sequence or as the translation. The program can also output the region around the START or the initial STOP codon or the ending STOP codons of an ORF for those doing analysis of the properties of these regions. The START and STOP codons are defined in the Genetic Code tables. A suitable Genetic Code table can be selected for the organism you are investigating.
Executable:
/getorf
Input Parameters:
 - Sequence
 - Start
 - End
 - Reverse
 - Ask
 - Nucleotide
 - Protein
 - Lower Case
 - Upper Case
 - Format
 - Database Name
 - Entry Name
 - UFO Features
 - Features Format
 - Features File
 - Output Format
 - Output Extension
 - Standard Output
 - Filter
 - Options
 - Debug
 - Verbose
 - Help
 - Report Warnings
 - Report Errors
 - Report Fatal Errors
 - Report Dying Program Messages
 - Output Base Filename
 - Turn Off Prompts
 - Output Database Name to Add
 - Separate File for Each Entry
 - Output UFO Features
 - Output Features Format
 - Output Features Filename
 - Table
 - Minimum Nucleotide Size of ORF
 - Maximum Nucleotide Size of ORF
 - Find
 - Don't Start Codons at Methionine
 - Circular Sequence
 - No Reverse
 - Flanking
Output Parameters:
 - Output Sequence
 - Output Directory
 - Output Features Directory
File size:33.21 KB
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