TITLE: ORFanID Web-based Search Engine to Identify Orphan and Taxonomically Restricted Genes
AUTHORS: Thushara Galbadage, Vinodh Gunasekera, Emanuel Tundrea, Richard S. Gunasekera

[DESCRIPTION]
ORFanID is a web-based software engine designed to identify ORFan genes from genomes of interest; from a given list of DNA or protein sequences within the NCBI databases. The selection of the taxonomy level of interest can define the scope of the search for orphan genes. Detectable homologous sequences are found by the software for candidate genes in the NCBI databases. Based on these findings, the ORFanID engine identifies and depicts orphan genes. Results may be viewed and analyzed graphically for scientific research and inquiry. As the enigma of orphan genes unravels, we believe ORFanID will provide critical insights into the origin, function, and prevalence of ORFan genes in genomes.

The last step contains a supplemental video with extra context and tips, as part of the protocols.io Spotlight series, featuring conversations with protocol authors.

[STEPS]
SECTION: Accessing ORFanID
1. Navigate to ORFanID's webpage at http://www.orfangenes.com/
SECTION: Accessing ORFanID
2. Click "Get Started" on the home page to access the search system.

  

SECTION: Input Methods
4. Choose between searching for a gene sequence or using an accession number. For instance, to search a Homo sapiens sample, use the toggle switch to specify your preference.
SECTION: Input Methods
5. ORFanID offers three search methods:
a.	Uploading a FASTA file.
b.	Inputting an accession number or numbers. (e.g., the E. coli sample has three given accession numbers)
c.	Directly submitting gene sequences.
SECTION: Search Guidelines
6. When searching multiple gene sequences, separate each with a new line or space.
SECTION: Search Guidelines
7. You'll need to specify the organism for your search. If the desired organism isn't listed, refer to the NCBI taxonomy database to obtain its full scientific name and taxonomy ID. Enter this information, ensuring the taxonomy ID is in parentheses.
SECTION: Search Guidelines
8. Choose between searching by protein or gene using the provided radio selection boxes.
SECTION: Additional Options
9. There's an optional Nickname field on the upper left. Use it to label and identify your search results for future reference.
SECTION: Additional Options
10. Adjust the three advanced parameters if needed. By default, the maximum e-value for the BLAST algorithm is set to three, and the maximum target sequences are set at 550. Hover over the pop-up for detailed info.
SECTION: Submission and Results
11. After confirming your search criteria, the organism, and any other fields, click "Submit". A pop-up will prompt you to review your search. If satisfied, proceed to submit. Depending on the complexity of your query, results may take between 3 to 15 minutes.
12. You'll be redirected to the "Results" tab. A light green box indicates that processing is ongoing. Once complete, it turns dark green. To view your results, click the graph icon on the right of the results table.

  

SECTION: Sample Searches
3. If you don't have a specific gene sequence or an accession number, use the sample options provided. Four sample icons are located at the bottom left of the search screen. Clicking on any of these will pre-fill the input field with either a gene sequence or an accession number. Click "Search" to proceed.
SECTION: Spotlight video
13.