note - FIZ Karlsruhe

Sequence Code Match Searching
Exact Sequence Search of Proteins (/SQEP) retrieves protein sequences that exactly match the
search query. The search query must be completely defined. Variability symbols are not allowed.
Subsequence Search of Proteins (/SQSP) retrieves exact answers plus sequences in which the
query sequence is embedded. Variability symbols are allowed.
Exact Sequence Search of Nucleic Acids (/SQEN) retrieves nucleic acid sequences that exactly
match the search query. The search query must be completely defined. Variability symbols are not
allowed. Ambiguity codes are allowed.
Subsequence Search of Nucleic Acids (/SQSN) retrieves exact answers plus sequences in which
the query sequence is embedded. Variability symbols are allowed. Ambiguity codes are allowed.
Exact Family Sequence Search of Proteins (/SQEFP) retrieves protein sequences that exactly
match the query and answers in which family-equivalent substitution of the query amino acids
occurs (see table below). Variability symbols are not allowed.
Subsequence Family Search of Proteins (/SQSFP) retrieves exact sequences, subsequences, and
answers in which family-equivalent substitution of the query amino acids occurs (see table below).
Variability symbols are allowed.
Amino acid families for SQEFP and SQSFP
The SQEFP and SQSFP family code match options for GETSEQ searching, allow narrow
variability searching based upon highly conservative substitutions of chemically similar amino
acids. The amino acid families are shown in the table below.
Group Amino Acids
Neutral - weakly hydrophobic P, A, G, S, T
Acid amine - hydrophilic Q, N, E, D, B, Z
Basic - hydrophilic H, K, R
Hydrophobic I, M, L, V
Aromatic F, W, Y
Cross-linking C
Neutral - weakly hydrophobic P, A, G, S, T
Acid amine - hydrophilic Q, N, E, D, B, Z
Basic - hydrophilic H, K, R
Hydrophobic I, M, L, V
Aromatic F, W, Y
GENESEQ on STN (DGENE) Workshop Manual | Page 103