SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   Bioinformatics (http://seqanswers.com/forums/forumdisplay.php?f=18)
-   -   install local blast (http://seqanswers.com/forums/showthread.php?t=13721)

shuang 08-26-2011 11:50 AM

install local blast
 
I tried to install local blast on my Linux machine. However, I don't see blastn, nor blastx, not blastp. Why??

commands:

>wget ftp://ftp.ncbi.nih.gov/blast/executa...4-linux.tar.gz

>tar zxvf blast-2.2.25-x64-linux.tar.gz

up to this step, under the directory of blast-2.2.25/bin/, I see those files below

-rwxr-xr-x 1 3755 5333 7202584 2011-01-30 09:32 bl2seq
-rwxr-xr-x 1 3755 5333 7191857 2011-01-30 09:32 blastall
-rwxr-xr-x 1 3755 5333 6511061 2011-01-30 09:32 blastclust
-rwxr-xr-x 1 3755 5333 6758201 2011-01-30 09:32 blastpgp
-rwxr-xr-x 1 3755 5333 6812336 2011-01-30 09:32 copymat
-rwxr-xr-x 1 3755 5333 6490648 2011-01-30 09:32 fastacmd
-rwxr-xr-x 1 3755 5333 6498981 2011-01-30 09:32 formatdb
-rwxr-xr-x 1 3755 5333 6803192 2011-01-30 09:32 formatrpsdb
-rwxr-xr-x 1 3755 5333 6503411 2011-01-30 09:32 impala
-rwxr-xr-x 1 3755 5333 6494292 2011-01-30 09:32 makemat
-rwxr-xr-x 1 3755 5333 7183659 2011-01-30 09:32 megablast
-rwxr-xr-x 1 3755 5333 7169549 2011-01-30 09:32 rpsblast
-rwxr-xr-x 1 3755 5333 6538067 2011-01-30 09:32 seedtop

empyrean 08-26-2011 11:59 AM

I guess you are missing something.. the above 'fastacmd' and 'formatdb' are from older version of blast. 2.2.25 version is blast+ and you should see 'blastdbcmd' and 'makeblastdb' for fastacmd and formatdb. and you will find blastn and blastp under bin only. Try to install in a new location.

kmcarr 08-26-2011 12:36 PM

You downloaded from the older format C toolkit BLAST. To get the newer, C++ toolkit BLAST+ suite you should use this URL:

Code:

ftp.ncbi.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.25+-x64-linux.tar.gz
(I wrapped it in CODE tags so the board software would not try to automagically create a link. Copy this link and paste in another window if you want to download.)

macrowave 08-27-2011 02:14 PM

just run blastall you'll see all the options, these are the old blast programs, now it's called blast+ suit, as mentioned above.

dnusol 09-07-2011 12:39 AM

Hi,

When downloading databases for local blast, I realized NCBI does not hold uniprot database in their site. Is it possible to download uniprot from uniprot.org and use it in blastx? Do I have to format it somehow or does blast recognize it as it is?

Thanks for your help

Dave

GenoMax 09-07-2011 04:13 AM

Dave,

You can download the uniprot fasta sequences from: http://www.uniprot.org/downloads

You will need to format and create blast indexes before you can use uniprot to blast against. You can find the help manual for blast here: http://www.ncbi.nlm.nih.gov/books/NBK52636/


Quote:

Originally Posted by dnusol (Post 50768)
Hi,

When downloading databases for local blast, I realized NCBI does not hold uniprot database in their site. Is it possible to download uniprot from uniprot.org and use it in blastx? Do I have to format it somehow or does blast recognize it as it is?

Thanks for your help

Dave


brojee 07-07-2019 07:53 AM

You can download the uniprot fasta successions from: http://www.uniprot.org/downloads

You should organization and make impact lists before you can utilize uniprot to impact against. You can discover the assistance manual for impact here: http://www.ncbi.nlm.nih.gov/books/NBK52636/


All times are GMT -8. The time now is 08:27 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.