note - FIZ Karlsruhe

VII: Variability Symbols for GETSEQ
Appendices
There are many symbols which can be used in DGENE RUN GETSEQ subsequence
searches /SQSP,/SQSFP and /SQSN (page 102), to allow for variability in residues. These
symbols facilitate the searching of motifs, domains or other conserved regions, in either
peptide or nucleotide sequences. The full table of options is given below.
Symbol(s) Function Search Example
[ ] Specify alternate residues
[-]
{ }
with a
number or
range
?
*
+
Exclude a specific residue or
alternate residues
Repeat the preceding symbol,
sequence, or an L-number, Enumber
or saved name for a
sequence query
Repeat the preceding symbol,
sequence, or sequence query
zero or one time
Repeat the preceding symbol,
sequence, or sequence query
zero or more times
Repeat the preceding symbol,
sequence, or sequence query
one or more times
LGP[VL]/SQSP:
LGP followed by either V or L
ATTGC[-A]GAAG/SQSN:
ATTGC followed by any
nucleotide except A followed
by GAAG
GG(FL){1-3}/SQSP
(or GG(FL){1,3}/SQSP):
GGFL, or GGFLFL, or
GGFLFLFL.
CAT(CTG){1,}TATT/SQSN:
CAT followed by one or more
repetitions of CTG followed by
TATT, e.g. CATCTGTATT,
CATCTGCTGTATT,
CATCTGCTGCTGTATT etc.
FLRRI(RP)?K/SQSP is
equivalent to
FLRRI(RP){0,1}K/SQSP:
FLRRIK or FLRRIRPK
CAT(CTG)*TATT/SQSN is
the same as
CAT(CTG){0,}TATT/SQSN:
CATTATT or CAT followed
by any number of repetitions of
CTG followed by TATT, e.g.
CATCTGTATT,
CATCTGCTGTATT etc.
CAT(CTG)+TATT/SQSN is
equivalent to
CAT(CTG){1,}TATT/SQSN:
CAT followed by one or more
repetitions of CTG followed by
TATT, e.g. CATCTGTATT,
CATCTGCTGTATT,
CATCTGCTGCTGTATT etc.
GENESEQ on STN (DGENE) Workshop Manual | Page 135