alternative start codons

[cpaight]

Is it possible to set spaln parameters when running ProtHin? I want to specify the translation table I want spaln to use.

[tomasbruna]

There is no interface to do this, but you can change them directly in here:

ProtHint/bin/spalnBatch.sh

Lines 60 to 62 in 0385924

	"$binDir/../dependencies/spaln" $mode $nonCanonicalFlag -LS -pw -S1 -O1 -l $alignmentLength "$nuc" "$prot" \
	2> /dev/null | "$binDir/../dependencies/spaln_boundary_scorer" -o "${nuc}_${prot}" -w 10 \
	-s "$binDir/../dependencies/blosum62.csv" -e $min_exon_score -x $min_exon_score