Candida albicans Genome Pattern Matching

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Candida albicans 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 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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Enter a

sequence or pattern (examples):

Choose a Sequence Database (click and hold to see the list):

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: 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 GLFZ
X or . Any amino acid DXXXDN..R
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:
[ ] A subset of elements [WFY]XXXDN[RK][ST]
[^ ] An excluded subset of elements NDBB...[VILM]Z[DE]...[^PG]
( ) Specifies a sub-pattern GG(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' end sjgo> (pep)
yattrtga> (nuc)

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	GLFZ
X or .	Any amino acid	DXXXDN..R
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:
[ ]	A subset of elements	[WFY]XXXDN[RK][ST]
[^ ]	An excluded subset of elements	NDBB...[VILM]Z[DE]...[^PG]
( )	Specifies a sub-pattern	GG(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' end	sjgo> (pep) yattrtga> (nuc)

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

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