Question: blast local database
1
gravatar for dllopezr
20 months 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 • 889 views
ADD COMMENTlink modified 20 months ago by h.mon29k • written 20 months ago by dllopezr60
3
gravatar for h.mon
20 months ago by
h.mon29k
Brazil
h.mon29k 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 20 months ago by h.mon29k

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 20 months ago by genomax76k
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 20 months ago • written 20 months ago by h.mon29k

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

ADD REPLYlink written 20 months 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 20 months ago by genomax76k
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