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10.9 years ago
HG
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Hi everyone, I want to check whether proteins are contained in assembled contigs or not ?
For this After De-novo assembly I made a local data base of contig file, which are in fasta formate :
makeblastdb -in contigsH131.fasta -dbtype nucl -out ecolidb.db
In next step i want i tried tblastn and getting some error message like:
./tblastn -num_threads 2 -comp_based_stats F -query refence.fasta -db ecoli.db -out report.bls
Error msg
BLAST Database error: No alias or index file found for nucleotide database [ecoli.db] in search path [/home/hiren/Desktop/test/ncbi-blast-2.2.28+/bin::
Can anyone please help me out.
Thank you so much.
Have you tried to set the complete db path? It's like the program is looking it up in the blast bin directory.
No i did not set . Because my working path in bin directory and database also present in bin. So do you think should i set complete path??
If I were you, I'd first predict proteins, and then create a protein db to blast against. Anyway, in your makeblastdb command you call the db "ecolidb.db" and then you try to blast against "ecoli.db". There's your problem.
Ok I appreciate your idea. If i am correctly understand you idea : i will predict the protein of reference genome first and make a local protein db then i will blast my contig.db against it. Please correct me if i am wrong ..
Sorry, what I meant to write is that first you predict proteins from your contigs with e.g. FragGeneScan, and then you blast them against a protein db, e.g. nr or refseq_protein, or maybe some more specific db that might serve your goals better. The upside of blasting against nr or refseq_protein is that you can link your hits to KO numbers (if you have access to KEGG FTP) and then see also what modules/pathways are present..
Trying according to your suggestion but getting some error any idea:
No clue, I'm using this version of FGS. If you're predicting from contigs, the command is: ./FragGeneScan -s contigs.fasta -o FGS -w 1 -t complete
ok ...let me check and let you know
Error is like that: any idea
Is that with the "mg-rast" version I linked, or the one from http://omics.informatics.indiana.edu/FragGeneScan because I also had segmentation errors with the latter..
its: http://omics.informatics.indiana.edu/FragGeneScan/