Help with Standalone Blast

Ash · 08-19-2010, 07:42 AM

Hi all,

I have managed to install standalone blast on my computer and it appears to be working correctly. The output file I get (and I have tried a number of different options) never tells me the number of hits my query has against the database I have created, unlike the online ncbi version of blast - is there any way to make standalone blast tell you this?

Also, it seems to make no difference changing the "-v" and "-b" parameters. I know from the online version that I should be getting approximately 4500 hits, but I don't seem to be able to get standalone blast to display them all - any thoughts as to how I can make it do this?

All help gratefully received!

PS this is using blastall -p blastn

maubp · 08-19-2010, 08:46 AM

Quote:

Originally Posted by Ash

PS this is using blastall -p blastn

That means you are using the old "legacy" BLAST written in C, not the new BLAST+ tools written in C++, which is what the NCBI website is running now.

Also whenever you get different results to the website, check the parameters carefully. Quite often the website uses different defaults for things like gap settings.

Ash · 08-23-2010, 05:14 AM

Many thanks for your response.

The parameters are identical in the 2 searches (online and standalone) - I think perhaps the difference is that I'm using legacy blast and not the BLAST+ that the NCBI website is running.

Can anyone running the new BLAST+ (standalone) tell me if it will
i) Give you the number of hits against your database (like the online BLAST does)?
ii) Allow you to relatively easily create your own databases to search (I note from the literature that the formatdb command has been replaced with the makeblastdb command?
iii) Will databases created with the older legacy BLAST be usable with the new BLAST+?

All help gratefully received!

A

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08-19-2010, 07:42 AM	#1
Ash Member Location: UK Join Date: Jun 2010 Posts: 15	Help with Standalone Blast Hi all, I have managed to install standalone blast on my computer and it appears to be working correctly. The output file I get (and I have tried a number of different options) never tells me the number of hits my query has against the database I have created, unlike the online ncbi version of blast - is there any way to make standalone blast tell you this? Also, it seems to make no difference changing the "-v" and "-b" parameters. I know from the online version that I should be getting approximately 4500 hits, but I don't seem to be able to get standalone blast to display them all - any thoughts as to how I can make it do this? All help gratefully received! PS this is using blastall -p blastn

08-23-2010, 05:14 AM	#3
Ash Member Location: UK Join Date: Jun 2010 Posts: 15	Many thanks for your response. The parameters are identical in the 2 searches (online and standalone) - I think perhaps the difference is that I'm using legacy blast and not the BLAST+ that the NCBI website is running. Can anyone running the new BLAST+ (standalone) tell me if it will i) Give you the number of hits against your database (like the online BLAST does)? ii) Allow you to relatively easily create your own databases to search (I note from the literature that the formatdb command has been replaced with the makeblastdb command? iii) Will databases created with the older legacy BLAST be usable with the new BLAST+? All help gratefully received! A