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Find Nested Alternate ORFs (nAlt-ORFs) (version 0.1.2)

Gene BED:

A BED file with 12 columns

Source for Genomic Sequence Data:

Select reference genome:

Minimum length of peptide translation to report:

Only report the first unique occurrence of an alternate sequence:

Do not report any alternate sequences that match a provided canonical CDS:

A BED file with 12 columns

Translation table:

Create log file:

Find Nested Alternate Open Reading Frames (nAlt-ORFs).

Using a BED12 file containing the location of genes, and a matching reference genome, this tool searches in the alternate reading frames of the provided canonical coding sequence, and outputs nested alternate ORFs which match the provided thresholds.

Translation table identifiers are based upon NCBI standards (https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi).