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

PatMatch [1] enables you to search for short (<20 residues) nucleotide or peptide sequences, and for sequence patterns. You can search against collections of nucleotide or peptide sequences drawn from a single organism or multiple organisms. Peptide and Nucleotide sequences can also be drawn from a SmartTable. In addition, you can define a list of organisms in a SmartTable, and perform pattern searches against the proteomes or genomes of those organisms. In addition you can define a list of proteins or list of genes in a SmartTable, and perform pattern search against these proteins or genes.

PatMatch 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 characters with no degenerate positions, please use Search > BLAST Search, which is much faster. Currently the smallest acceptable input is 3 characters and the maximum number of results is 250,000.

First you will specify what set of sequences to search across, then you will specify what pattern(s) to search for.

[x] Search across sequences from which source?
The full E. coli K-12 substr. MG1655 E. coli

Note: if you create a user account and log in, you can perform pattern searches against nucleotides and organisms in SmartTable.

Note: if you create a user account and log in, you can perform pattern searches against proteins and organisms in SmartTable.


Search which strand(s):

Enter the sequence or pattern to search for (examples):

or

PLEASE WAIT FOR EACH REQUEST TO COMPLETE BEFORE SUBMITTING ANOTHER.

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

Supported Sequence and Pattern Syntax and Examples

The pattern you provide is a series of characters from the following table. Some characters match only themselves in the matching sequence (e.g., AGTC), whereas other characters are wildcards that can match multiple characters in the matching sequence. For example,
  • The sequence "AATTGC" can match only the sequence "AATTGC" because none of those characters are wildcards.
  • The pattern "RRYY" will match two purine bases followed by two pyrimidine bases. For example, it can match:
    • AACC
    • AATT
    • AGTC

Search Type Character Meaning Example Patterns Containing Character
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)

[1] Yan, T., et al., PatMatch: a program for finding patterns in peptide and nucleotide sequences, Nucleic Acids Res. 2005.

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