I am working on Transcriptome sequencing of fungi. I would like to find pathogenecity related genes from fungi. HPI database provides this information, but I do not know how to make a blast or mapping using this data base as it provides only txt file of all the genes?
Depending on your software access, this can be pretty easy. I've used CLC Genomics Workbench and Geneious for similar tasks. If you can download the HPI database as a .fasta file, then you'll be able to create a custom BLAST database in CLC or Geneious. Once you have your BLAST database set up, you can BLAST your transcriptome very easily. I've done this A TON - let me know if you have any questions!
Thank you for your kind reply. But i can't find fasta file of this data base. Actually in download section on site http://www.phi-base.org/ there is only a text file containing list of accession numbers. Can you please send me the link from where i can download fasta file of PHI data base?.
Sorry if I was unclear - I was not sure if you'd be easily able to download a fasta file from this database-it appears you can't. I would suggest trying to use the NCBI database to do a batch download of all the sequences in this PHI database using the accession IDs which are included in the text file you found.
Ok i will try. But again the problem is that all the sequences are not from NCBI and include sequences from EMBL and Uniport also , but yet i will try. Thank you.
Thank you Dr Kevin, i have execrated all the sequences by running some scripts.
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