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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, Onl J Bioinform.,
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.