PatMatch search for E. coli K-12 substr. MG1655

Pattern Matching allows you to search for short (<20 residues) nucleotide or peptide sequences, or ambiguous/degenerate patterns. Pattern Matching is not a replacement for BLAST. It allows for ambiguous characters, mismatches, insertions and deletions, but does not perform alignments. If you are searching sequences larger than 20 residues with no degenerate positions, please use Search > BLAST Search, which is much faster. Currently the smallest acceptable input is 3 residues and the maximum number of results is 250,000.

[x] Enter a sequence or pattern ( examples ):
If DNA, Strand:

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

or

PLEASE WAIT FOR EACH REQUEST TO COMPLETE BEFORE SUBMITTING ANOTHER.


More Options
Maximum hits:
Maximum Hits per Sequence:
Minimum Hits per Sequence:
Number of Mismatches allowed:
Mismatch Type:
or

Supported Pattern Syntax and Examples:

Search Type Character Meaning Examples
Peptide Searches IFVLWMAGCYP TSHEDQNKR Exact match DQGT
J Any hydrophobic residue (IFVLWMAGCY) AAAAAAJJ
O Any hydrophilic residue (TSHEDQNKR) TTTTTTOO
B D or N FLGB
Z E or Q GLFGZ
X or . Any amino acid DXXXNW..VSK
Nucleotide searches ACTGU Exact match ACCGGCGTAA
R Any purine base (AG) AAGGCCGGRRRR
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 CCGG...WHW.{3,5}HWH...CCGG
H A or C or T
D A or G or T
B C or G or T
N or X or . Any base ATGCTNNNNATCG
All searches: [ ] A subset of elements
[TC] = T or C
[WFY]XXXDN[RK][ST]
[^ ] An excluded subset of elements
[^TA] = not T or A,
(matches nucleotides C or G)
NDBB...[VILM]Z[DE]...[^PG]
( ) Specifies a sub-pattern
(YPT) = YPT
(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}DGZ
< Constrains pattern to N-terminus or 5' end of the target <MNTD (pep)
<ATGX{6,10}RTTRTT (nuc)
> Constrains pattern to C-terminus or 3' end of the target sbgz> (pep)
yattrtga> (nuc)

Report Errors or Provide Feedback
Page generated by Pathway Tools version 22.0 (software by SRI International) on Fri Sep 21, 2018, BIOCYC15.
EcoCyc version 22.0.