[Bioperl-l] Doubt - Regarding Stand Alone Blast

[Dave Messina]

Hi Teja,

Please 'reply all' to keep the mailing list Cc'd so that it can be archived
and everyone can follow along.




On Tue, May 3, 2011 at 13:45, sukeerthi teja Rallapalli <tejaminnu at gmail.com
> wrote:

> Hi David,
>
> I basically have these 2 files, the
>
> Input file        = sequences.txt
> Database file  = homologene_result.txt
>
> Isn't "blastall" an older version command ? That is why i was using
> makeblastdb
>

In your previous email, you made the same mistake with both formatdb and
makeblastdb. (making a database for one file but specifying the other file's
name as the database when you tried to run blast)




> This is what i typed
>
> 172-30-8-231:bin sukeerthiteja$ makeblastdb -in homologene_result.txt
> -dbtype prot -parse_seqids -out teja1 blastp -query sequences.txt -db teja2
>

You've combined two separate commands on the same line here.

This is one command:
makeblastdb -in homologene_result.txt -dbtype prot -parse_seqids -out teja1

This is another command:
blastp -query sequences.txt -db teja2

Incidentally, this blastp again won't work because you've named your datase
teja1 when you run makeblastdb, but then you tell blastp that the database
is named teja2. Instead, you should do

blastp -query sequences.txt -db teja1

because that's the name you specified with the -out option to makeblastdb.


Two things:
#1 You need to read the NCBI-BLAST+ documentation available here:
http://www.ncbi.nlm.nih.gov/books/NBK1763/

#2 This is the BioPerl mailing list, and your questions do not relate to
BioPerl. seqanswers.com is probably a more appropriate place to ask them.
But I would suggest doing #1 first.


Dave





AND i also tried the code using .txt next to *teja2.txt, * but in both cases
> i got this error.
>
> Error: (106.18)
> NCBI C++ Exception:
>     Error: (CArgException::eSynopsis) Too many positional arguments (1),
> the offending value: blastp
>     Error: (CArgException::eSynopsis) Application's initialization failed
>
Thanking you
> Teja
>