I have a problem with blastx against database nr.

Question

[weimabri]

-Hello

-I built the database for the nr with the following command

$ makeblastdb -dbtype prot -in nr

-which went well and generated .pal .psq files. phr

-then I ran the blastx with the following command

$blastx -db nr -query /home/danielurrea/Escritorio/RNAseq_Aegypti_ibague/Trinity_clean_Com13.Trinity.fasta

-generating this error

$BLAST Database error: No database names were found in alias file [/home/danielurrea/Escritorio/nr/nr].

In advance thanks for the help

Answer 1

[GenoMax]

For the names to work you need to use --parse_seqids option when you create the database. Why are you building your own indexes? If this is straight nr then download the pre-made indexes NCBI makes available on FTP site.