Question: blast local database
1
gravatar for dllopezr
2.4 years ago by
dllopezr60
dllopezr60 wrote:

Hi everyone

I need to locate a blast local database that was created on s server long time ago, but i don't know what is it extension or how it looks if I see it through more command.

How I can find this file?

blast • 1.2k views
ADD COMMENTlink modified 2.4 years ago by h.mon31k • written 2.4 years ago by dllopezr60
3
gravatar for h.mon
2.4 years ago by
h.mon31k
Brazil
h.mon31k wrote:

At its simplest form, blast databases have three files: for nucleotides, file.nhr, files.nin, file.nsq; for proteins, file.phr, files.pin, file.psq. Search for one of these extensions:

find . -name "*.phr"
ADD COMMENTlink written 2.4 years ago by h.mon31k

It may be better to extend that across the entire file system since OP does not know where the files are.

find / -name "*.phr"
ADD REPLYlink written 2.4 years ago by genomax89k
1

In this case, it is better to redirect stderr to /dev/null, or the screen will be flooded with "permission denied" messages:

find / -name "*.nhr" 2>/dev/null

Another option is to use some find magic to avoid searching over files / dirs where one doesn't have permission:

find / -type d ! -perm -a+x -prune -type f ! -perm -a+r -prune -o -type f -name '*.phr' -print

Reference: How do I remove “permission denied” printout statements from the find program?

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by h.mon31k

thanks for your help. If I want to make blast vs this local database, which of these files I must use?

ADD REPLYlink written 2.4 years ago by dllopezr60

You will use the basename of the file. e.g. if file is called nt.phr then you will use nt.

ADD REPLYlink written 2.4 years ago by genomax89k
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