Yeast Genome Pattern Matching

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.

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: Insertions Deletions Substitutions

Supported Pattern Syntax and Examples:

Search type	Character	Meaning	Examples
Peptide Searches
	IFVLWMAGCYP TSHEDQNKR	Exact match	ELVIS
	J	Any hydrophobic residue (IFVLWMAGCY)	AAAAAAJJ
	O	Any hydrophilic residue (TSHEDQNKR)	GLFGO
	B	D or N	FLGB
	Z	E or Q	GLFGZ
	X or .	Any amino acid	DXXXDN..RQS
Nucleotide searches
	ACTGU	Exact match	ACGGCGTA
	R	Any purine base (AG)	AATTTGGRGGR
	Y	Any pyrimidine base (CT)	CCCATAYYGGYY
	S	G or C	YGGTWCAMWTGTY
	W	A or T
	M	A or C
	K	G or T
	V	A or C or G	CGG...WH.{3,5}HW...CCG
	H	A or C or T
	D	A or G or T
	B	C or G or T
	N or X or .	Any base	ATGCNNNNNATCG
All searches
	[ ]	A subset of elements	[WFY]XXXDN[RK][ST]
	[^ ]	An excluded subset of elements	NDBB...[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' end	sjgo> (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.

Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied. The SGD project at Stanford University is supported by a Genome Research Resource Grant from the US National Human Genome Research Institute, part of the US National Institutes of Health.