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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. -
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?Comment
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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.Comment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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Here are nine questions we think about, in roughly the order they matter, before...
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