ORFanGenes Instructions

1. How to Run an Example Sequence

1. Visit the ORFanGenes website and click on "Input" from the Navigation bar, or "Get Started" at the bottom of the page.
2. Click on the "Example" link on the bottom left. The text fields will automatically get filled with an example input sequence of genes of E. Coli.
3. The E-Value defaults to e-3 and the Maximum Target Sequences for BLAST defaults to 1000. If these need to be changed, "Advanced Parameters" can be selected and move the slider to select the appropriate values.
4. Select "Submit" and wait for around 10 minutes or more until ORFanGenes processes the input sequence and returns the results.
5. View the results of the example sequence

The example input contains three genes. Out of the three genes, two of which are Genus Restricted Genes, and the other is an ORFan Gene. The Blast Results table shows the taxonomies (and their parents) for each gene in the input sequence from the BLAST search.

2. Using ORFanGenes

1. Visit the ORFanGenes website and click on "Input" from the Navigation bar, or "Get Started" at the bottom of the page.
2. Select the type of sequence (Protein or Nucleotide) that will be processed.
3. Click “Browse” and upload a sequence file. The file must be in .fasta format, and must contain the geneid value of each gene
4. Begin typing the input organism’s name and select the name from the suggested results, and select the organism from the dropdown menu.
5. Select “Advanced parameters” and adjust the maximum E-value and maximum target sequences for BLAST.
6. Click “Submit” and wait for results to load. The time taken for the results to be obtained is dependent on the number of input sequences, selected e-value, and number of target sequences.