Yeast Genome Pattern Matching Help



Pattern Matching allows you to search for short (<20 residues) nucleotide or peptide sequences, or ambiguous/degenerate patterns. It uses the same dataset as SGD's BLAST program. If you are searching for a sequence >20 bp or aa with no degenerate positions, please use BLAST, which is much faster. Pattern Matching allows for ambiguous characters, mismatches, insertions and deletions, but does not do alignments and so is not a replacement for BLAST. Please note, also, that PatMatch will not find overlapping hits.

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Choose a genome to search:

Enter a sequence or pattern (examples):

Choose a Sequence Database (click and hold to see the list):
All public S. cerevisiae sequences can be found within these datasets.

or

PLEASE WAIT FOR EACH REQUEST TO COMPLETE BEFORE SUBMITTING ANOTHER. These searches are done on a single computer at Stanford shared by many other people.


More Options :
Maximum hits:
If DNA, Strand:
Mismatch: (more information on use of the Mismatch option)
Mismatch Type:

Supported Pattern Syntax and Examples:

Search typeCharacterMeaningExamples
Peptide Searches
IFVLWMAGCYP
TSHEDQNKR
Exact matchELVIS
JAny hydrophobic residue (IFVLWMAGCY)AAAAAAJJ
OAny hydrophilic residue (TSHEDQNKR)GLFGO
BD or NFLGB
ZE or QGLFGZ
X or .Any amino acidDXXXDN..RQS
Nucleotide searches
ACTGUExact matchACGGCGTA
RAny purine base (AG)AATTTGGRGGR
YAny pyrimidine base (CT)CCCATAYYGGYY
SG or CYGGTWCAMWTGTY
WA or T
MA or C
KG or T
VA or C or GCGG...WH.{3,5}HW...CCG
HA or C or T
DA or G or T
BC or G or T
N or X or .Any baseATGCNNNNNATCG
All searches
[ ]A subset of elements[WFY]XXXDN[RK][ST]
[^ ]An excluded subset of elementsNDBB...[VILM]Z[DE]...[^PG]
( )Specifies a sub-pattern(YDXXX){2,}
{m,n}{m} = exactly m times
{m,} = at least m times
{,m} = 0 to m times
{m,n} = between m and n times
L{3,5}X{5}DGO
<Constrains pattern to N-terminus or 5' end<MNTD (pep)
<ATGX{6,10}RTTRTT (nuc)
>Constrains pattern to C-terminus or 3' endsjgo> (pep)
yattrtga> (nuc)

Limits on the use of the Mismatch option

At this time, the mismatch option (Insertions, Deletions, or Substitutions) can only be used in combination with exact patterns that do not contain ambiguous peptide or nucleotide characters (e.g. X for any amino acid or R for any purine) or regular expressions (e.g. L{3,5}X{5}DGO). In addition, the mismatch=3 option can only be used for query strings of at least 7 in length.