Query Features BMT

There are multiple query sequence formats in the Biomolecule Toolkit to filter both natural and unnatural sequences.

Natural analogue sequences are entered by 1-letter codes, unnatural sequences are entered by multi-letter codes using dot separators between the building blocks.

Example for natural sequence query: SEQUENCE

Example for unnatural sequence query: S.dE.Q.U.dE.N.C.dE

Note: the searches in Biomolecule Toolkit are case-insensitive (e.g. dS is equal to ds)

Available wildcards

‘N’ for nucleic acid sequences

‘X’ for amino acid sequences

‘*’ for 1, 2… n residues in nucleic acid or amino acid sequences

Note: oligonucleotide backbone modifications cannot be queried currently.

Table 1. Single residue wildcards (amino acid sequences)

Query sequence	Target sequence
	HCAYKAMGNMAMCAQRTPY (wild type)	HCAYAAMGNMAMCAQRTPY (mutation)	HCAYKAMGNMAMCAQRTPYK (insertion)	HCAYKAMGNMAMCAQRTPY (deletion)
HCAYXAMGNMAMCAQRTPY

Table 2. Multi-residue wildcards (amino acid sequences)

Query sequence	Target sequence
	HCAYKAMGNMAMCAQRTPY (wild type)	HCA K KAMGNMAMCAQRTPY (mutation)	HCAYKAMGN K MAMCAQRTPY (insertion)	HCAYKAMGNMA MCAQRTPY (deletion)	HCAYK AYK AMGNMAMCAQRTPY (duplication)
HCAY*QRTPY
HCAYMGNMQRTPY
HCAYMAQRTPY
HCAXKAM*QRTPY