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G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
Published on: March 22, 2018
Optimal clone identifier for genomic shotgun libraries: "OC Identifier tool".
M E Cantão1, J E Ferreira, E G M Lemos
1Departamento de Ciência da Computação, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, SP, Brasil. cantao@ime.usp.br
Genetics and Molecular Research : GMR
|December 7, 2007
Summary
This study introduces the OC Identifier tool, which uses genomic shotgun libraries to identify unique genes for DNA microarrays, even with partially sequenced genomes. This bioinformatics approach streamlines gene selection for transcriptome and phylogeny studies.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- DNA microarrays typically use synthesized oligonucleotides for gene amplification via PCR.
- Shotgun library sequences offer an alternative for studying individual genes within a genome.
Purpose of the Study:
- To develop a bioinformatics tool, OC Identifier, for identifying unique genes in genomic shotgun libraries.
- To enable microarray analysis using shotgun clones without a fully sequenced genome.
Main Methods:
- Utilized shotgun library sequences and a partially sequenced genome.
- Developed the OC Identifier tool for comparative genome analysis.
- Integrated query language for relational databases and bioinformatics tools.
Main Results:
- The OC Identifier tool successfully identifies unique genes within shotgun libraries.
- Facilitates the selection of genes for DNA microarray construction.
- Enables simultaneous use of clones in transcriptome and phylogeny studies.
Conclusions:
- OC Identifier provides an alternative to primer synthesis for gene identification in microarray construction.
- Supports comparative genomic hybridization and genome assembly projects.
- Streamlines gene analysis during the genome sequencing phase.
