BioSCAN: a network sharable computational resource for searching biosequence databases

Abstract

We describe a network sharable, interactive computational tool for rapid and sensitive search and analysis of biomolecular sequence databases such as GenBank, GenPept, Protein Identification Resource, and SWISS-PROT. The resource is accessible via the World Wide Web using popular client software such as Mosaic and Netscape. The client software is freely available on a number of computing platforms including Macintosh,

Bio-sequence database scanning on a GPU

“…P-NAC was the first such machine and computed edit distance over a four-character alphabet [11]. More recent examples, better tuned to the needs of computational biology, include BioScan [18], BISP [4], and SAMBA [6].…”

Massively parallel solutions for molecular sequence analysis

“…However, they are limited to one single algorithm, and thus cannot supply the flexibility necessary to run a variety of algorithms required analyzing DNA, RNA, and proteins, e.g. P-NAC, SAMBA, Bioscan [11,5,17]. Reconfigurable systems are based on programmable logic such as field-programmable gate arrays (FPGAs), e.g.…”

“…There are two basic methods of mapping the scanning of protein sequence databases to a parallel processor: one is based on the systolisation of the sequence comparison algorithm, the other is based on the distribution of the computation of pairwise comparisons. Systolic arrays have been proven as a good candidate structure for the first approach [5,17], while more expensive supercomputers and networks of workstations are suitable architectures for the second [10]. This paper presents two solutions to high performance database scanning on two new architectures: a hybrid parallel computer and the Fuzion 150.…”

High performance biosequence database scanning on reconfigurable platforms

“…P-NAC was the first such machine and computed edit distance over a four-character alphabet [16]. More recent examples, better tuned to the needs of computational biology, include BioScan, BISP, and SAMBA [5,12,18].…”

“…There are two basic methods of mapping the scanning of sequence databases to a parallel processor: one is based on the systolisation of the sequence comparison algorithm, the other is based on the distribution of the computation of pairwise comparisons. Systolic array architectures have been proven as a good candidate structure for the first approach [5,12,18], while more expensive supercomputers and networks of workstations are suitable architectures for the second [7,15].…”