[Bioclusters] Condor cluster and BLAST

[David Adelson]

Paul,

If you are interested in all vs all comparisons there are other  
tools, depending on what it is you are after.  if you want to find  
things that have identical bits (overlaps,duplicates...) you might  
want to consider MUMMER (see the TIGR software download web page or  
sourceforge.net), which is super fast, gives you perfect matches,  
snps, indels and such and will probably only need a single  
workstation to run, even for thousands of sequences. The downside is  
that you get no stats and the output format is "user indifferent" if  
not downright "user hostile".  In spite of this I am a big fan of  
MUMMER for these kinds of searches.  If you want to find the perfect  
matches AND less than perfect matches, BLAT may work for you provided  
you dial in the settings appropriately.  If you want the above and  
some stats you probably should use a BLAST or FASTA.  If you have  
time to spare and want the best stats for the alignments FASTA wins  
hands down.

my 2c.

Dave Adelson, Texas A&M University

Outside of a dog, a book is man's best friend. Inside of a dog it's  
too dark to read.

Groucho Marx


On Jan 25, 2006, at 12:41 PM, Paul wrote:

> Great response for Sandy. I am in a similar position with a new  
> cluster in our lab. I am still very early in the learning curve and  
> your comments for Sandy are very helpful. We have and all vs all  
> Blast job that we would like to run. I am trying to get a handle on  
> how best to run this. I am wondering if you have any comments  
> regarding all vs all tools. I am aware of blastn but was  
> considering maybe Blat instead. We are mainly interested in high  
> homology hits and the increased speed of Blat might be of value. Do  
> you have any experience with Blat? If so how difficult do you think  
> it would be to use it in an all vs all setup. Any comments would be  
> great. I am a bit over my head at the moment. Thanks
> We have rocks 4.1 installed along with the biobrew roll. Currently  
> we have about 14 cpus.
>
> Paul Mc Kenna
>
>
>
> Christopher Dwan wrote:
>
>> Sandy,
>>
>> First the nitty gritty:
>> --------------------------
>> * I recommend using the binary downloads at ftp:// 
>> ftp.ncbi.nih.gov/ blast/. If computation is ever the limiting  
>> factor on your system then switch over to custom binaries.
>>
> (snip)
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