3.2.3 ORF
An ORF(s) is the part of a reading frame that can be translated. The ORF (potential protein-coding sequence) is a continuous stretch of codons that usually begins with a start codon and ends at a stop codon. Understanding ORF(s) has become a piece of essential evidence to assist in gene prediction. As with other ORF finding tools, easyfmperforms a six-frame translation of a nucleotide given a particular genetic code, finding all ORFs possible. Long ORFs are often used, along with other evidence, to initially identify candidate protein-coding regions or functional RNA-coding regions in a given DNA sequence, but the presence of an ORF does not necessarily mean that the region is always translated (Deonier et al., 2005). As BLAST and BLAT, the web-based ORF Finder (https://www.ncbi.nlm.nih.gov/orffinder/), ORF Predictor (http://bioinformatics.ysu.edu/tools/OrfPredictor.html) and command-line tools (ORF Investigator (Dwivedi & Mishra, 2012) and orfipy (Singh & Wurtele, 2021) offer a range of ORF searches, but its usage can be challenging for biologists due to lack of computer programming literacy and limited query sequence length. To maximise the flexibility, the easyfm ORF provides a fast and efficient approach for all possible translation and extraction of ORFs from nucleotide sequences (FASTA format of nucleotide and protein output from six-frame translation) (Figure 4). With a simple mouse click solution, users can compare the translated outcomes with their biological evidence to avoid false discovery as well as control specific parameters without any limitation of query sequence length. Along with existing tools (Dwivedi et al., 2012; Singh & Wurtele, 2021), easyfm ORF will provide rapid, flexible searches in multiple output formats to allow the easy downstream analysis of ORFs.