CGD Pattern Matching

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Pattern Matching allows you to search for short (<20 residues) nucleotide or peptide sequences, or ambiguous/degenerate patterns. It uses the same datasets as CGD BLAST. 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):
NOTE: Sequence Database options may be limited by Genome and peptide/nucleotide choices , above.

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:
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 QGLFZ
X or .Any amino acidDXXXDN..R
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 searchesa:
[ ]A subset of elements[WFY]XXXDN[RK][ST]
[^ ]An excluded subset of elementsNDBB...[VILM]Z[DE]...[^PG]
( )Specifies a sub-patternGG(DGXX){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<MNY (pep)
<ATGX{6,10}RTTRTT (nuc)
>Constrains pattern to C-terminus or 3' endsjgo> (pep)
yattrtga> (nuc)

a. At this time, patterns containing regular expressions do not support the mismatch, deletion and insertion options.


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