I'm an undergraduate student completing a capstone project working to characterize a plant microbiome. I have a couple thousand fungal ITS sequences in a fasta file. Is there any way to analyze these in bulk besides individually BLASTing sequences by the 20's? I'm trying to find the probable identity of these organisms. Thanks!
1. What we did for a similar problem is used the BLAST+ command line tool
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download
2. AND then automated the process via a python code for multiple sequences.
Chakit Arora Thank you so much! I've downloaded BLAST+, but did you create a reference genome set or use the outsourcing command for your analysis? Also, would you mind sharing the python code to automate the process? Thanks again for being such a great help!
@Kyle Parker
You don't need any kind of code...Since you have already installed Blast+
You just need to get reference fungal sequence database... Nucleotide sequences or protein sequences...
Makeblate database with makeblast command
And run blast or blastx command (based on your reference database) with your ITS sequences as input query file.
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