ORF Marker plugin: UGENE - Integrated Bioinformatics Tools

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ORF Marker plugin

ORF Marker is an utility that finds regions of the given length without stop codons in DNA sequence. The regions found can be stored as annotations to the sequence.

To activate the utility use "Analyse->Find ORFs" menu in sequence view:

The dialog will appear where you can select strands, DNA sequence region to search, translation code and minimal ORF length:

Notes:

DNA-to-Amino translation table defines the way start and stop codons are encoded.
ORFs with length lower than "Min length" value will not be shown in report.
Dropping the check for "Must start with init codon" item switches ORF Marker algorithm to the mode when any non-stop amino acid code is interpretted as region start position.

After search is finished you can browse the results, sort them by length, strand or start position and save as annotations to the original sequence in Genbank format.