Reconfigurable systems for sequence alignment and for general dynamic programming
Genet. mol. res. (Online)
;
4(3): 543-552, 2005. ilus, graf, tab
Article
Dans Anglais
| LILACS
| ID: lil-444957
ABSTRACT
Reconfigurable systolic arrays can be adapted to efficiently resolve a wide spectrum of computational problems; parallelism is naturally explored in systolic arrays and reconfigurability allows for redefinition of the interconnections and operations even during run time (dynamically). We present a reconfigurable systolic architecture that can be applied for the efficient treatment of several dynamic programming methods for resolving well-known problems, such as global and local sequence alignment, approximate string matching and longest common subsequence. The dynamicity of the reconfigurability was found to be useful for practical applications in the construction of sequence alignments. A VHDL (VHSIC hardware description language) version of this new architecture was implemented on an APEX FPGA (Field programmable gate array). It would be several magnitudes faster than the software algorithm alternatives.
Texte intégral:
Disponible
Indice:
LILAS (Amériques)
Sujet Principal:
Algorithmes
/
Logiciel
/
Alignement de séquences
/
Biologie informatique
Type d'étude:
Étude pronostique
Limites du sujet:
Humains
langue:
Anglais
Texte intégral:
Genet. mol. res. (Online)
Thème du journal:
Biologie moléculaire
/
Génétique
Année:
2005
Type:
Article
Pays d'affiliation:
Brésil
/
Allemagne
Institution/Pays d'affiliation:
Technische Universität Kaiserslautern/DE
/
Universidade de Brasília/BR
Documents relatifs à ce sujet
MEDLINE
...
LILACS
LIS