Find Sequences - Motif

Find sequences that match your query, which can be a protein/nucleotide string.

1. Enter or copy and paste a protein/nucleotide string. See Motif Patterns.
2. Select the appropriate Sequence Type based on your query.
3. Check the Include NCBI Sequences box to include those sequences with NCBI (National Center for Biotechnology Information) database entries.
4. Under Advanced Biosequence Search, you may change the default Query Coverage % and E-Value selections as well as check the Combine Motif Results option to return a single, unified set of results across all variants.
5. Click the Search Sequences button.
   
   

You will then arrive back on the Home page where you may View Results and status for individual searches.

Important: Sequence results expire 30 days after the date they are first generated.

Motif Patterns

Amino Acid Codes

Creates a positive scoring mismatch for amino acids (e.g., A sequence query with a B will retain the B, and the B will score positively against D or N in the hit subject sequence).

Degenerate Code	Logical Meaning
X	Any amino acid
B	D or N
Z	E or Q
J	I or L

Nucleotide Codes

Generates multiple queries for nucleotides where the degenerate code is replaced by the nucleotides it represents.

Degenerate Code	Logical Meaning
N	A or C or G or T
R	A or G
Y	C or T
M	A or C
K	G or T
S	C or G
W	A or T
H	A or C or T
B	C or G or T
V	A or C or G
D	A or G or T

Regex Syntax

Degenerate Code	Logical Meaning
.	Translated to X for protein Enumerates to A, G, C, and T for nucleotide (generates four search terms)
{m,n}	At least m and maximum n residues length
{n}	Exactly n length
[XYZ]	Any nucleotide or amino acid listed within the square brackets
^XYZ$	Search for the exact sequence XYZ