Makeblastdb problem

[detq182]

i just download a secuence in .FASTA format from uniprot but
i cant make it work, this are the errors.

makeblastdb -in Arabidopsis_thaliana.fas -parse_seqids -dbtype prot
BLAST Database error: No alias or index file found for protein database [Arabido
psis_thaliana.fas] in search path [C:\blast-2.2.25+;C:\blast-2.2.25+\db;]

makeblastdb -in swissprot.fas -dbtype prot -out Thaliana
Error: Unable to open input swissprot.fas as either FASTA file or BLAST db

makeblastdb -in swissprot.fas -dbtype prot -out Thaliana.db
Error: Unable to open input swissprot.fas as either FASTA file or BLAST db

Please help......

[Kennels]

check your downloaded sequences for whether they are truly in fasta format. the errors are complaining that it isn't

[detq182]

thanks Kennels, but how can i check it ? the downloaded sequences said Arabidopsis_thaliana.Protein.fasta

[Kennels]

On the command line, type

head -n 4 <name of your fasta file>

what do the headers and sequence look like?

[GenoMax]

It appears that detq182 is doing this on a windows machine.

@detq182: Are you using cygwin to do this or natively in windows itself?

[detq182]

On the command line, type

head -n 4 <name of your fasta file>

what do the headers and sequence look like?

Cant do the command line. head command dont recognise.

[detq182]

It appears that detq182 is doing this on a windows machine.

@detq182: Are you using cygwin to do this or natively in windows itself?

Yes im on windows and natively not using cygwin.

please help.....

[detq182]

I finally can do it

comman line:
makeblastdb -in \blast-2.2.25+\db\uniprot_sprot.fasta -parse_seqids -dbtype prot

and done, thank all of you for your time.

[jp.]

Hi
Can someone please explain me how to make blast database in details.
I have downloaded the following dir and kept under wd:
1. wd/ncbi-blast-2.2.29+
2. wdblast
3. wd/blast/nr
4. wd/blast/nt
5. wd/blast/other genomic

I get the error:
BLAST Database error: No alias or index file found for nucleotide database [blast/nt] in search path [wd/blast/nr]
BLAST Database error: No alias or index file found for nucleotide database [blast/nt] in search path [wd/blast/nt]
thank you

[GenoMax]

It is not clear if you have downloaded the pre-made indexes for nr/nt etc from NCBI (ftp://ftp.ncbi.nlm.nih.gov/blast/db/) though you made the directory structure above.

[jp.]

Yes, I have downloaded from there only all the database.
But the problem is that I dont know how to make database, the files are there in the exact PATH but program can not find it cos database is prepared and balst is not installed so blast can not read these files , thats my problem...

[GenoMax]

Yes, I have downloaded from there only all the database.
But the problem is that I dont know how to make database, the files are there in the exact PATH but program can not find it cos database is prepared and balst is not installed so blast can not read these files , thats my problem...

Forgive me if the following is redundant but I am not clear about what you are trying to say above.

The blast executables are available here: ftp://ftp.ncbi.nlm.nih.gov/blast/exe...blast+/2.2.29/ Get the one that is appropriate for your OS. Once those are uncompressed you should be good to go forward.

[jp.]

I m sorry for not mentioning exactly before. The blast executable was downloaded from here only: ftp://ftp.ncbi.nlm.nih.gov/blast/exe...blast+/2.2.29/ for linux64 bit. However, I dont have problem in blast executables. and the database for blast (such as nr, nt, other genomic) were ftp://ftp.ncbi.nlm.nih.gov/blast/db/

The problem is, while running the blast, it can not read the database files (nr, nt, other genomics) in the PATH (./blast/nr, ./blast/nt, ./blast). Eventhough, these files are at same PATH but blast executable can not read it and give error stating that can not find these files in the following PATH (./blast/nr, ./blast/nt, ./blast). Because, I think, I did not generated blast databse using blast+/2.2.29/bin/.. commands. I think, I need to make database and then indexes (but I think, I downloaded pre-built indexes) and do something that blast+/2.2.29/ can read the database files...
????

[mastal]

If you have downloaded pre-built databases, then you don't need to make a database.

Have a look at the blast manual:

http://www.ncbi.nlm.nih.gov/books/NBK1763/

You need to set a variable BLASTDB with the path to the blast databases,
or else specify the complete path to the database, starting from the root directory.

[jp.]

I think so that pre-built db needs only PATH. and I did as follows:
dir structure
PATH=$PATH:wd/ncbi-blast-2.2.29+/bin
PATH=$PATH:wd/blast
PATH=$PATH:wd/blast/nr
PATH=$PATH:wd/blast/nt
PATH=$PATH:wd/blast
I get the error:
BLAST Database error: No alias or index file found for nucleotide database [blast/nt] in search path [wd/blast/nr]
BLAST Database error: No alias or index file found for nucleotide database [blast/nt] in search path [wd/blast/nt]

that is my problem...????