Sequence searching

Using wildcards

The sequence query can use wildcards

  • * - match zero or more characters
  • ? - match exactly one character

So, to find chains that start with "GIVE" use the query "GIVE*". Likewise, to find chains that end with "NYCN" use the query "*NYCN".

To find chains that contain the subsequence "VEQC" use the query "*VEQC*".

Note that you should use "?" as a wildcard for "any residue" - not "X". The "X" is used by Proteax as a placeholder in the plain sequence for residues or linkers that cannot be said to have a natural equivalent.

Searching cyclic chains

When a chain is cyclic the query will always be converted to a contains/subsequence query, since there is no fixed starting point of a cyclic chain.

Therefore the query "TLVG" will match both the cyclic chain

(cyclo)-DTLVGAS-(cyclo)

as well as

(cyclo)-VGASDTL-(cyclo)