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Bioinformatics FAQ
There are a large number of bioinformatics programs available to CBRG account holders via this web site. These
examples (Frequently Asked Questions) are used to illustrate the use of these tools
in answering typical queries posed by researchers.
The major web-based tools from the CBRG are listed, here.
How do I search for a defined pattern within a protein sequence?
Program name: fuzzpro
Notes: This program will search for a particular pattern (or "signature") of amino acids - exact matches or
ambiguities.
Patterns are written in PROSITE format (more information about PROSITE
patterns).
Example: Searching for the isocitrate lyase signature...
K - [KR] - C - G - H - [LMQR]
...within a protein sequence (UniProt_SwissProt:PRPB_ECOLI) gives the following result.
Example output from fuzzpro
# Report_format: dbmotif
#=======================================
# Sequence: PRPB_ECOLI from: 1 to: 295
# HitCount: 1
#
# Pattern: K - [KR] - C - G - H - [LMQR]
# Mismatch: 0
#=======================================
Length = 6
Start = position 120 of sequence
End = position 125 of sequence
DQVGAKRCGHRPNKAI
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120 125
Further reading: fuzzpro background
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