Find out motif
4
0
Entering edit mode
5.2 years ago

How to search a motif in an entire genome using bioinformatics tool? For eg. if I want to find out hydrophobin (eight-cysteine) with a characteristic pattern of 1-2-1-1-2-1 in fungi (say in Bipolaris maydis, B. victoriae, Fusarium graminearum and Phyphthora infestans) how to do it?

Motif • 1.2k views
ADD COMMENT
1
Entering edit mode
5.2 years ago
GenoMax 102k

If you have protein sequences available then you can use fuzzpro from EMBOSS: http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/fuzzpro.html

ADD COMMENT
0
Entering edit mode

You can use it on Galaxy and get the genomes directly from UCSC or Biomart.

ADD REPLY
0
Entering edit mode
5.2 years ago

Thank you so much. But how can I search my query motif in the entire genome of the pathogen?

ADD COMMENT
0
Entering edit mode
5.2 years ago
natasha.sernova ★ 3.8k

See C: Identification of a given amino acid sequence in nucleotide sequence,

tblastn is easy.

My anwers to this lady may help you, I hope.

ADD COMMENT
0
Entering edit mode

You study fungi-genomes, right?

ADD REPLY
0
Entering edit mode
5.2 years ago

Oh right. I missed that. Thank you so much. Ya fungi-plant interaction in context of effector proteins.

ADD COMMENT
0
Entering edit mode

You have nucleotide contigs, I hope,

so you can easily make a database from them with makeblastdb

and search it with tblastx or tblastn,

as I wrote here. C: Identification of a given amino acid sequence in nucleotide sequence

Good luck!

ADD REPLY

Login before adding your answer.

Traffic: 2784 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6