Supplementary Figure 5: Plass ORF extraction and start codon prediction (ORF calling).
From: Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold
Plass extracts two sets of ORFs. ORF set 1 contains all translated ORFs with at least 45 codons. ORF set 2 contains all translated ORFs with at least 20 codons starting with a putative ATG start codon that is the first ATG codon after a stop codon in the same frame. (Start codon prediction) Plass predicts start codons with a consensus method using a multiple sequence alignment of ORF set 1 and 2. Wherever at least 20% of all methionines in one column are marked by a prepended asterisk, it removes the preceding residues from all other sequences and prepends an asterisk to all sequences to mark the start.
