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Question: FASTA sequences not blasting.
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gravatar for gbernard
3 months ago by
gbernard • 0
gbernard • 0 wrote:

Hello Great Minds,

My FASTA sequences ( in tabular format) are not blasting. I downloaded the UNIPROT fasta.gz file to use as a database. Please provide some direction.

Best regards. GCB
rna-seq • 213 views
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written 3 months ago by gbernard • 0
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gravatar for gb
3 months ago by
gb • 60
gb • 60 wrote:

Not sure what you mean but this is already wrong:

My FASTA sequences ( in tabular format) are not blasting

Fasta is a certain format, first you have a line starting with ">" and a description and the next line is a sequence. https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=BlastHelp

So your file with sequences needs to be in in FASTA format not tabular. And would need to do a blastp.
ADD COMMENT • link written 3 months ago by gb • 60

Thank you so much! You are correct. The sequences are in fasta format with a Trinity header from the assembly. I downloaded the UNIPROT protein database and unzipped the file to compare against my sequences. Both are in FASTA format according to Galaxy. The issue now is to figure out what is the input value for the subject/database sequences and protein database section in the NCBI BLASTx. The protein database section reads "no Blast dbp available", I tried BLASTing my assembled reads against the UNIPROT database which is saved in my history and no results. Any suggestions? Is there a database I can import?

Best regards,

ADD REPLY • link written 3 months ago by gbernard • 0

I am not familiar with the public servers so I can not help you more. But you need to mention which galaxy server you are using. Also check the input, before you can blast against a reference you need to index the reference fasta file. So basicly you convert a fasta file to a blast database.

EDIT:

I just checked https://usegalaxy.org and went to the tool named "NCBI BLAST+ blastx". You need to change the setting "Subject database/sequences" to "fasta file from history". You also need to check the genetic code setting.

And an other thing, I am not sure if this is the best approach. Uniprot is a large database and your trinity output probaly contains a lot of reads so I think it will take very long. Maybe you can reduce your input. Like removing the duplicates or something. You can also try diamond.

ADD REPLY • link modified 3 months ago • written 3 months ago by gb • 60
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