[maubp]

Yes, that's correct. But the output file generated is of random pattern which makes it more difficult for me to extract only aligned regions. Below if the example of the file.

Please let me know if anyone knows how to deal with this. Thank you!

BioPerl has a parser for this (the default plain text output from BLAST). You can also tell BLAST to output simple tabular data, or XML. Lots of options.

[horvathdp]

problems with stand alone blast to nr

Hi all. I downloaded blast, and can make it work fine when I blast one data set against another (after formatting them) , but I can't seem to get the program to do a blast against the nr database that I downloaded and unpacked. My command lines is: blastn -query C:\Users\horvathd\Desktop\DREB.fa -db nr -out C:\Users\horvathd\Desktop\Dreb_vs_nr.txt -evalue 1e-5 -num_alignments 20 -outfmt 0 -num_descriptions 20

I get the following error

BLAST Database error: No alias or index file found for nucleotide database [nr]
in search path [C:\Program Files\NCBI\blast-2.2.24+\bin;;]

I unpacked the nr files in the "bin" folder. I can blast the DREB.fa file against other databases I have created with no problem. Any idea what I am doing wrong?

[robs]

If you take a look at the error message, it tells you why: "No alias or index file found for nucleotide database [nr]". The NR database is a protein database. What you probably want is NT.