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?
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
Thank you so much. But how can I search my query motif in the entire genome of the pathogen?
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.
Oh right. I missed that. Thank you so much. Ya fungi-plant interaction in context of effector proteins.
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!
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version 2.3.6
You can use it on Galaxy and get the genomes directly from UCSC or Biomart.