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.