Optimized spaced seeds improve sensitivity and specificity in local homology search. Several authors have shown that multiple seeds can have better sensitivity and specificity than single seeds. We describe a linear programming (LP)-based algorithm to optimize a set of seeds. Theoretically, our algorithm offers a performance guarantee: the sensitivity of a chosen seed set is at least 70% of wha...

MOTIVATION Homology search finds similar segments between two biological sequences, such as DNA or protein sequences. The introduction of optimal spaced seeds in PatternHunter has increased both the sensitivity and the speed of homology search, and it has been adopted by many alignment programs such as BLAST. With the further improvement provided by multiple spaced seeds in PatternHunterII, Smi...

We will introduce a way how we can achieve high speed homology search by only adding one off-the-shelf PCI board with one Field Programmable Gate Array (FPGA) to a Pentium based computer system in use. FPGA is a reconfigurable device, and any kind of circuits, such as pattern matching program, can be realized in a moment. The performance is almost proportional to the size of FPGA which is used ...

Proteins evolve by mutations and natural selection. The network of sequence similarities is a rich source for mining homologous relationships that inform on protein structure and function. There are many servers available to browse the network of homology relationships but one has to wait up to a minute for results. The SANSparallel webserver provides protein sequence database searches with imm...

SUMMARY Detection of distant homology is a widely used computational approach for studying protein evolution, structure and function. Here, we report a homology search web server based on sequence profile-profile comparison. The user may perform searches in one of several regularly updated profile databases using either a single sequence or a multiple sequence alignment as an input. The same pr...