note - FIZ Karlsruhe

Appendices
Symbol(s) Function Search Example
^
Query appears at the beginning
or at the end of a sequence
| Alternate sequence expressions
. a gap of one residue
: a gap of zero or one residue
.{m}
or
.[m.]
.{m,u}
or
.{m-u}
.? or :
or
.{0,1}
or
.{0-1}
.*
or
.{0,}
or
.{0-}
.+
or
.{1,}
or
.{1-}
&
a gap of m residues
a gap of m to u residues
a gap of zero or one residue
A gap of zero or more residues
A gap of one or more residues
Concatenate 1 (join together)
sequences or queries
Page 136 | GENESEQ on STN (DGENE) Workshop Manual
^CATCTGTATT/SQSN:
CATCTGTATT at the
beginning of a sequence
ACD|KLM|TWA/SQSP:
ACD or KLM or TWA
SY.RPG/SQSP:
SY followed by one residue
followed by RPG
SY:RPG/SQSP:
SYRPG or SY followed by one
residue followed by RPG
SY.{2}RPG/SQSP:
SY followed by any 2 residues
followed by RPG
GFF.{2,10}LSS/SQSP: GFF
followed by a gap of 2 to 10
residues followed by LSS
AGA.?SRI/SQSFP is
equivalent to
AGA.{0,1}SRI/SQSFP: AGA
followed by zero or one
residue followed by SRI
HLC.*TYG/SQSP is
equivalent to
HLC.{0,}TYG/SQSP:
HLC followed by a gap of zero
or more residues followed by
TYG
SY.+TH/SQSP is equivalent to
SY.{1,}TH/SQSP:
SY followed by any number of
residues followed by TH
L1&L2&L3/SQSN:
the sequence in L1 followed by
the sequence in L2 followed by
the sequence in L3.
1 Can be used for /SQSN, /SQSP, /SQSFP queries but also for exact sequence searches /SQEP, /SQEFP and /SQEN