MeridianMERIDIAN

Protein Sequence

representation.scientific.protein_sequence

Amino acid sequence in single-letter IUPAC notation (20 standard amino acids plus ambiguity codes).

Worked samples

DuckDB 1.5.5 · finetype 0.6.64

ValueAs VARCHARlengthmolecular_weight_estimate
MKVLLIVGSMKVLLIVGS9990
ACDEFGHIKLMNPQRSTVWYFLACDEFGHIKLMNPQRSTVWYFL222420
MPKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGMPKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVG424620

Shape

Pattern
^[ACDEFGHIKLMNPQRSTVWXY*]+$
ValueLengthShape
MKVLLIVGS9matches
ACDEFGHIKLMNPQRSTVWYFL22matches
MPKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVG42matches
mkvllivgs9rejected: lower-cased

Told apart

1 of the 6 other scientific types accept every one of these samples on shape alone.

Going the other way, this type's own rule accepts 3 of 3 samples of DNA Sequence.

Standard: A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y Ambiguity: B (D or N), Z (E or Q), X (any), * (stop codon)

Background

Origin

The IUPAC-IUB Commission on Biochemical Nomenclature published A One-Letter Notation for Amino Acid Sequences in 1968.[1] The IUB-IUPAC one-letter recommendations were approved in 1968 on the basis of proposals of a subcommittee of W. E. Cohn, M. O. Dayhoff, R. V. Eck and B. Keil.[1] The possibility of using one-letter symbols for amino acids was mentioned by Gamow and Yčas in 1958.[1] Šorm and colleagues systematised the idea of one-letter amino acid symbols in 1961.[1] Dayhoff and Eck used one-letter symbols derived partly from the code of Šorm and colleagues in their compilations of protein sequences.[1] The IUPAC recommendations describe a one-letter code as much more concise than the three-letter system for presenting long protein sequences.[1] The IUPAC recommendations name aligning and comparing homologous sequences as one of the uses of the one-letter code.[1]

Where several amino acids shared an initial letter, the letter went to the most frequently occurring and structurally simplest of them: alanine (A), glycine (G), leucine (L), proline (P) and threonine (T).[1] F for phenylalanine and R for arginine were chosen for their phonetic associations.[1] Tryptophan was given W because the double ring of the molecule is associated with the bulky letter.[1] The IUPAC note on the choice of symbols says U was avoided because it is easily confused with V in handwritten material.[1] The IUPAC note on the choice of symbols says O was avoided because it could be confused with G, Q, C and D in imperfect computer print-outs, and also with zero.[1] J was avoided because it is absent from several languages.[1]

In the IUPAC code, X means that the identity of an amino acid is undetermined, or that the amino acid is atypical.[1]

Use

The FASTA format originated from the FASTA software package.[2] A sequence in FASTA format begins with a single-line description, marked by a greater-than symbol, followed by lines of sequence data.[3] NCBI recommends that all lines of text in FASTA input be shorter than 80 characters.[3] NCBI BLAST expects sequences to be written in the standard IUB/IUPAC amino acid and nucleic acid codes.[3] NCBI BLAST accepts lower-case letters and maps them into upper case.[3]

Where you'll meet it

UniProt documents the FASTA headers it uses for UniProtKB, UniRef and UniParc.[4] UniProtKB's FASTA file for entry P69905, human haemoglobin subunit alpha, gives the sequence in one-letter code beginning MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMF.[5]

Sources

  1. [1]Nomenclature and Symbolism for Amino Acids and Peptidesstandard
  2. [2]FASTA formatsecondary source
  3. [3]Query Input and database selection — BlastTopics 0.1.1 documentationdocumentation
  4. [4]FASTA headersorganisation
  5. [5]P69905.fastadataset

Detection notes

v1 migration: New for v2. Single-letter amino acid notation. Standard: A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y Ambiguity: B (D or N), Z (E or Q), X (any), * (stop codon)

Use it

CLI · DuckDB
$ finetype infer -i "MKVLLIVGS" --mode column
→ representation.scientific.protein_sequence

SELECT ft_infer('MKVLLIVGS');
-- → 'representation.scientific.protein_sequence'
Cast expression
UPPER(CAST({col} AS VARCHAR))

Schema

https://meridian.online/schemas/representation.scientific.protein_sequence · Frictionless type string

finetype taxonomy representation.scientific.protein_sequence -o json-schema

Aliases

proteinpeptideamino_acid_sequence

Type Registry