Copied from my LinkedIn message board.
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1000x faster BLASTX?
What would a 100 to 1000x speed up on BLASTX mean to your research project. No special hardware. No supercomputer. No Joke. One US-based genome center is already using the speed up to enable their huge metagenomics project. The question is, who else has a project that could benefit from this ability? I'd be thankful for your ideas.
Martin Gollery • If it has the same sensitivity and selectivity as BLASTX, then it could mean a great deal. Can you contact me at marty.gollery@gmail.com to tell more about it?
sucheta Tripathy • I will also be interested to know more about this particular BlastX.
Thanks
Sucheta
Thanks
Sucheta
Manish Gupta • Great ...................
Using jumping index algo?
Using jumping index algo?
John Clouston • sorry for the delay in answering questions... here are 3 answers.
Martin G - sensitivity and accuracy is tunable, similarity to BLASTX is a must for any product that looks to replace the 'gold standard'.
Jian - I don't know if the strategy is like Pattern Hunter or not actually as I have not used that product. The search technology is based on a prior nucleotide space search that was developed a few years ago called SLIM Search. It is a hash-based approach but with novel strategies to those that are more commonly used in NGS space.
Martin H - USearch is not advertizing 1000x speed up for BLASTX protein search. Actually the author of Usearch says on the website "Currently, translated search (like BLASTX and TBLASTX) is not supported, but I'm working on it" So maybe you have access to a beta version? Please let us know what you know about USearch and protein space.
Disclaimer - when I started this conversation 4 months ago I was employed by Real Time Genomics, the inventors of the RTG mapx product that gives the 100x to 1000x speed up on BLASTX. The product is in use at the Genome Center at Washington University with their Human Microbiome Project (HMP). I am no longer officially representing Real Time Genomics but I will keep answering your questions on this topic. If you contact Real Time Genomics directly, let them know how you heard about the application.
Martin G - sensitivity and accuracy is tunable, similarity to BLASTX is a must for any product that looks to replace the 'gold standard'.
Jian - I don't know if the strategy is like Pattern Hunter or not actually as I have not used that product. The search technology is based on a prior nucleotide space search that was developed a few years ago called SLIM Search. It is a hash-based approach but with novel strategies to those that are more commonly used in NGS space.
Martin H - USearch is not advertizing 1000x speed up for BLASTX protein search. Actually the author of Usearch says on the website "Currently, translated search (like BLASTX and TBLASTX) is not supported, but I'm working on it" So maybe you have access to a beta version? Please let us know what you know about USearch and protein space.
Disclaimer - when I started this conversation 4 months ago I was employed by Real Time Genomics, the inventors of the RTG mapx product that gives the 100x to 1000x speed up on BLASTX. The product is in use at the Genome Center at Washington University with their Human Microbiome Project (HMP). I am no longer officially representing Real Time Genomics but I will keep answering your questions on this topic. If you contact Real Time Genomics directly, let them know how you heard about the application.
Robert Edgar • I am the author of usearch and ublast. The group may be interested to know that I am now beta-testing a new variant of the ublast algorithm with the following new features: 1. translated search, 2. gapped alignments, 3. chaining of alignments across frame-shifts, 4. ORF identification and target coverage criteria. These features are designed with gene calling in next-generation meta-genomic reads, but can also be useful in other applications. You are welcome to contact me for more information at robert@drive5.com or visit http://drive5.com/usearch for more information and to sign up for updates via email.
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