This section would be cool if it had a negative option and stuff like,
hydrophobics use Z.
It sorts with a 2x penalty for stop and give precence to more equal distributions,
in case of a tie to less degenerate codons.
Accepts three letter code with first letter capital separated by a space,
or one letter with spaces or not — corner case: SER is Ser + Asp
+ Arg while Ser is Serine.
Please choose at least one amino acid
Primer design for deep mutational scanning
To make primers at the ends of the coding sequence, the neighbouring noncoding
sequence are required. Two options are available:
To give the upstream and downstream sequence separately.
To give a sequence with a start and end position. A variant of this is
to give the starting/end position as a short sequence to match as opposed
to a number.
Deepscan generates a list of partially overlapping QuikChange-based primers
aimed at constructing mutability landscapes using PCR. It iterates across
a DNA sequence, codon by codon and generates a primer pair that employs
the partially overlapping primer pair strategy (Xia et al., 2015 ).
Namely, the primers in a pair will have an user-defined overlap length
( e.g. 22 bp) centred around the codon to mutate and will have a 3’
overhand long enough to allow the region beyond the mutagenized codon to
anneal with the template above a given melting temperature, while taking
into account terminal GC clamp. The traditional Quikchange protocol (Agilent)
works poorly for codon mutants.
The serverside calculations use a Python 3 script obtainable from:
mutational scanning ).