Interested in BLAST? Whether you are investing in a server farm, large SMP system, or Tera-BLAST, I can help sift through the maze of conflicting claims and confusing costs. Many less experienced consultants ignore the total cost of ownership in order to follow what is trendy, or looks good on their resume. Are you looking at Gene-BLAST? This is a very powerful solution for some people, but it has limitations as well. Make sure you are using the right tool for the job.
BLAST may not be the right tool, anyway- have you seen PatternHunter? It is faster than BLAST, but more sensitive. Other people have tried to do this, but these guys got it right. Interested? Let me know, and I will consult with you as to whether this is the best thing for your needs.
How about HMMs? I have developed a set of protein family databases (TLFAMs) that have been shown to provide better alignments in most cases than PFAM. Once again, this is not without drawbacks. I can show you whether or not these models are right for you.
Protein models such as HMMs can be tremendous assets in your search arsenal. Be sure to use them appropriately, and you will be rewarded.
Whether you are interested in buying a server farm, SMP server, or DeCypher system, I can analyze your requirements and help you properly size your system. If you already have a DeCypher system, I can help you optimize your searches for your particular needs- in short, make the most of your investment and custom design a set of job templates that ensure you maximize the results you receive from your DeCypher. I wrote the documentation and nearly all of the bioinformatics whitepapers, posters and presentations for TimeLogic- see http://www.timelogic.com/ for details.If I am booked solid, the other key person for Bioinformatics consulting is Al Shpuntoff. Al knows everybody, and has worked on everything, and hiring him will simply make your stuff work better. His website is http://www.world.std.com/~AFS.
For Linux farms that save you money in the long term, not just the initial 'wow factor', you need Chris Dagdigian. Drop me a line, and I'll put you in touch.
For parallel algorithms on SMP servers, contact Southwest Parallel Software. They have optimized versions of algorithms like PHRAP and ClustalW, and can work with pretty much any system. Check out the SPS website at http://www.spsoft.com/.
"BX, not BS!"
-Jim Lindelien, CEO
of TimeLogic
Contact me at: MartinGollery@hotmail.com
THANK YOU FOR YOUR INTEREST!!
I am now looking at new consulting opportunities for custom sequence analysis solutions and microarray design and analysis. If I am not the best person for your particular application, I probably know someone who is, and will be happy to recommend them. Either way, drop me a line and I will help you out!
