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blast local database

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
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updated by h.mon h.mon • written by dllopezr • dllopezr

1 answer

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"
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written by h.mon h.mon

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

find / -name "*.phr"
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written by GenoMax GenoMax

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?

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written by h.mon h.mon

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

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written by dllopezr • dllopezr

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

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written by GenoMax GenoMax

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