MSA search inputs

An MSA search job takes one field: the list of protein chains to align. There are no database, sensitivity or pairing options. Every job searches the same databases with the same settings Chai-1 and Boltz-2 use, which is what lets the three tools share one cache.

Sequences

Each sequence is normalized before it is checked or searched:

1. Whitespace is removed and letters are upper-cased, so a pasted, line-wrapped sequence is accepted.
2. The result must contain only amino-acid letters (the 20 standard residues plus X, B, Z, U and O). Anything else, such as a FASTA header, digits, alignment gaps (-) or a SMILES string, is refused. A nucleotide sequence in A/C/G/T letters passes this check, because those are amino-acid letters too, and would be searched as a nonsense protein.
3. The result must be at most 5,000 residues.

The cache key is the SHA-256 of the normalized sequence, so the same chain typed in lower case or with line breaks still hits the cache.

Example

The two chains of human insulin, aligned separately:

{
  "sequences": [
    "GIVEQCCTSICSLYQLENYCN",
    "FVNQHLCGSHLVEALYLVCGERGFFYTPKT"
  ]
}

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