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OJB©
Online Journal of
Bioinformatics©
Volume 4 :
96-105, 2003
Matching
carbohydrate-binding domains in Arabidopsis
thaliana genome:
development of a lectin database
Moreno FB1, Facó F1, Ceccatto
VM2, Sampaio
AH3, Costa ASB1, Freitas
JLT1, Nogueira
LL1, Lima ME4, Lima-Filho
JL5, Cavada
BS1*
1Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza-CE Campus do Pici S/N CEP: 60451-970 Caixa Postal 6033 Brasil. 2Universidade Estadual do Ceará (UECE). 3Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Fortaleza-CE, 4LIKA – Universidade Federal do Pernambuco (UFPE), 5Cin – Universidade Federal do Pernambuco(UFPE) *Correspondence bscavada@ufc.br
ABSTRACT
Moreno FB, Facó F, Ceccatto VM, Sampaio AH, Costa
ASB, Freitas JLT, Nogueira LL,
Lima ME, Lima-Filho JL, Cavada
SB., Matching carbohydrate-binding domains in Arabidopsis thaliana
genome: development of a lectin database, Online J
Bioinformatics, 4: 96-195, 2003.
Processing of databases used for homology searching requires great computational
power. Processing time can be reduced by integrating
databases. PERL was used to filter specific sequences from a
non-redundant protein database by counting and classifying sequences
taxonomically. A regular expression was matched against a string. The script
was used to build the first lectin database with
1,639 sequences entries in FASTA format. The program was applied to the
analysis of Arabidopsis thaliana
genome. All the unclassified open reading frames from this genome were
catalogued and analyzed by homology searching. Six possible proteins containing
carbohydrate domains were found. The proposed lectin
database and PERL scripts could be used as a generic proteomic tool.
KEYWORDS: lectin, Arabdopsis, database, genome, proteome.