Transcript finishing initiative: contribuição do laboratório IL2
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Data
2003-02-25
Autores
Ferrasi, Adriana Camargo [UNESP]
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Universidade Estadual Paulista (Unesp)
Resumo
O principal objetivo na análise de um genoma é a identificação gênica. Várias ferramentas computacionais estão disponíveis para este propósito e são baseadas em similaridade (BLAST e BLAT) ou em predição de genes (Genscan e Fgenes). Entretanto, estes programas estão se mostrando ineficientes para detectar e caracterizar todos os genes presentes no genoma humano. A importância das informações de cDNAs tem sido reconhecida desde o início do Projeto Genoma Humano, entretanto, o seqüenciamento em larga escala de cDNAs completos ainda requer técnicas avançadas tais como a produção de bibliotecas de cDNAs enriquecidas por transcritos grandes e raros. O seqüenciamento parcial de etiquetas de seqüências expressas (ESTs) foi desenvolvido como uma técnica alternativa para gerar, em larga escala, vários tipos de cDNAs. Atualmente, a maioria das informações de cDNAs no GenBank são representadas por ESTs convencionais 3þ e 5þ e ORESTES (provenientes das porções centrais dos transcritos). Baseados nos bancos de dados gerados pelo alinhamento de todas essas seqüências com as seqüências genômicas humanas disponíveis foi proposta a estratégia transcript finishing para a caracterização e validação de novos genes humanos, como parte do consórcio entre FAPESP e Instituto Ludwig de Pesquisa sobre o Câncer. O projeto Transcript Finishing Initiative está sendo realizado por uma rede de 31 diferentes grupos de pesquisa do Estado de São Paulo. Foram selecionados pela coordenação do projeto, 602 transcritos e destes 300 (50%) foram validados. Destes transcritos, 20 foram atribuídos ao laboratório validador IL2, e destes, 11 (55%) foram validados. Utilizando ferramentas de bioinformática, o laboratório IL2 realizou uma anotação preliminar dos consensos de seus transcritos validados (disponibilizados pela coordenação do projeto)... .
A fundamental task in analyzing genome is gene identification. This is relatively straightforward for compact genome but much more challenging for complex genomes. Some computational tools are available for this purpose, but they are bases on similarity (BLAST) or prediction analysis (Genscan and Fgenes). However, these programs are inefficient to detect and characterize all genes present in the genome. The importance of cDNA information has been recognized since the beginning of the Human Genome Project, however cost-effective and hightroughput sequencing of full-length cDNA still requires technical advances such as the production of cDNA libraries enriched for large and rare transcripts. Partial sequencing of expressed sequences (EST) has been developed as an alternative approach for the generation, in large-scale, of several kinds of cDNAs. Currently, the vast majority of cDNA data in the GenBank is represented both by conventional 5þand 3þexpressed sequence tags (ESTs) and by ORESTES (open reading frame ESTs), which is derived from central portions of the transcripts. Based on a database generated through alignment of all of these sequences to the available human genomic sequences, have been proposed the transcript finishing strategy for characterization and validation of new human genes, as part of the FAPESP-LICR Transcript Finishing Initiative. The strategy utilizes the ORESTES scaffold EST sequence to build primers for reverse transcription (RT) - PCR reactions in order to bridge gaps, thereby confirming the membership of ESTs to a common transcript and providing information on the intervening sequence (validation strategy). The FAPESP-LICR Transcript Finishing Initiative is being pursed by a network of 31 different research groups from the State of São Paulo (The Transcript Finishing Consortium) coordinated by 2 different laboratories... (Complete abstract click electronic address below).
A fundamental task in analyzing genome is gene identification. This is relatively straightforward for compact genome but much more challenging for complex genomes. Some computational tools are available for this purpose, but they are bases on similarity (BLAST) or prediction analysis (Genscan and Fgenes). However, these programs are inefficient to detect and characterize all genes present in the genome. The importance of cDNA information has been recognized since the beginning of the Human Genome Project, however cost-effective and hightroughput sequencing of full-length cDNA still requires technical advances such as the production of cDNA libraries enriched for large and rare transcripts. Partial sequencing of expressed sequences (EST) has been developed as an alternative approach for the generation, in large-scale, of several kinds of cDNAs. Currently, the vast majority of cDNA data in the GenBank is represented both by conventional 5þand 3þexpressed sequence tags (ESTs) and by ORESTES (open reading frame ESTs), which is derived from central portions of the transcripts. Based on a database generated through alignment of all of these sequences to the available human genomic sequences, have been proposed the transcript finishing strategy for characterization and validation of new human genes, as part of the FAPESP-LICR Transcript Finishing Initiative. The strategy utilizes the ORESTES scaffold EST sequence to build primers for reverse transcription (RT) - PCR reactions in order to bridge gaps, thereby confirming the membership of ESTs to a common transcript and providing information on the intervening sequence (validation strategy). The FAPESP-LICR Transcript Finishing Initiative is being pursed by a network of 31 different research groups from the State of São Paulo (The Transcript Finishing Consortium) coordinated by 2 different laboratories... (Complete abstract click electronic address below).
Descrição
Palavras-chave
Biologia molecular
Como citar
FERRASI, Adriana Camargo. Transcript finishing initiative: contribuição do laboratório IL2. 2003. xiii, 170 f. Dissertação (mestrado) - Universidade Estadual Paulista, Instituto de Biociências de Rio Claro, 2003.