hi, i use UGENE and i find that is a very good help!

now im searching for proteins domains using hmmsearch against the proteome, the fasta/gb file is a list of proteins with the sequence, but what i need is to locate them in the genome, because i am working with domains, i dont think i could have problems with introns/exons. also, the translation of the file is quite possible, but how can i annotate the results of my hmmsearch in the genome??

Hi Alekos,

Could you please provide detailed step-by-step description of your work?
What is the difference between hmm search in fasta/gb files and hmm search in some 'genome'?

Thank you!

well, im working looking for kinases involved in resistance genes in cassava, the thing is: i generate an hmm, hmmsearch in the proteome, and then, i want to locate those proteins in the genome
so i need the complete sequences of the hmmsearch result (it gives me only the sequences of the domains)
i had to do hmmsearch from console, output a table, import in a spreadsheet, copy.paste the protein names, search for those protein sequences with a perl script from mothur, and im refining the tblastn parameters
but hmm, i dont know if im doing something wrong, but the output of a hmmsearch made with ugene is the entire proteome!!

thank you in advance

Hi Alekos,


Quote:

dont know if im doing something wrong, but the output of a hmmsearch made with ugene is the entire proteome!!

Could you please send us example of data files you use so we can reproduce the issue with 'entire proteome'?

As of finding complete sequences of found domains, it looks like a perfect task for UGENE Workflow Designer.
You can draw a schema, where domain sequences from HMM Search block are extracted using Sequence Splitter module and after that send to NCBI BLAST.