I have query file which i got from genemarkhmm tool and which is in nucleotide format. My problem is I want to run BLASTx but It gives me "No alias or index file found for protein database" error. Mt database is protein database. I struck here help me this work is very important for me.
Hi, you used this link?! http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
Cheers, Nadine
Thanks Nadine A. Gund and Ka-Chun Wong for your replays . Actually I somehow find that formatdb command is used for the conversion, but not sure. And Nadine A. Gund, I didn't used that link because that is for protein query but I have nucleotide query so I cant use this, moreover I have to use stanalone tool.
Vishal - you only said you are using a Nucleotide query. What exactly do you want to search for? Is your target database that of proteins (nr)? Or is it that of nucleic acids (nt)? It is difficult to give an answer to your question without knowing that.
Thansks Karthikeyan for take interest, My query is nucleotide and database is nr(protein). I have contig sequences of S.pneumoniae.
Hi Vishal,
since you are working with bacterial sequences, predict ORF, translate into protein and use blastp. That would be the easiest for you.
@Neha, thanks for solution. However, I found that what was the problem actully I didn't converted into suitable format. For this I used formatdb command.
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools