Biomotif sequence patterns
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Walkthrough

learn the tool on a real sequence, one step at a time

Sequence

fetch from a database, paste FASTA, or open a file
Upstream and species apply to Ensembl gene and region lookups; a species is written like mus_musculus, and a misspelt one is reported as such. Search accepts NCBI field syntax, so HBB[gene] AND human[orgn] beats a bare name.
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Motif

a pattern is an expression, so it can be read, edited and checked
Example requests

Pattern-writing examples, grouped by compatible alphabet—not promises of a match in the loaded sequence.

The pattern language
"GAATTC"
a literal, on both strands; U and T are the same base
(iupac "TATAWAWR")
a nucleotide consensus with ambiguity codes
(prosite "N-{P}-[ST]-{P}")
a protein pattern in PROSITE syntax
(seq A B C)
the parts one after another
(alt A B C)
any one of them
(gap 15 19)
15 to 19 of anything
(run "CT" 8 20)
a run of 8 to 20 pyrimidines
(repeat M 3 6)
M repeated 3 to 6 times
(named 'box M)
M, reported separately under that label
(fuzzy 2 M)
a fixed-width M with up to 2 mismatches
(edit 1 "GAATTC")
up to 1 substitution, insertion or deletion
(hairpin (stem 5 10) (loop 3 8))
a stem-loop whose stem really base-pairs
at-start   at-end
sequence boundaries

What this means

written for someone who does not already know the biology

Results