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ProSplicer: a database of putative alternative splicing information derived from protein, mRNA and expressed sequence tag sequence data.

Huang HD, Horng JT, Lee CC, Liu BJ - Genome Biol. (2003)

Bottom Line: ProSplicer is a database of putative alternative splicing information derived from the alignment of proteins, mRNA sequences and expressed sequence tags (ESTs) against human genomic DNA sequences.Proteins, mRNA and ESTs provide valuable evidence that can reveal splice variants of genes.The alternative splicing information in the database can help users investigate the alternative splicing and tissue-specific expression of genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science and Information Engineering, National Central University, Jung-Li City 320, Taiwan.

ABSTRACT
ProSplicer is a database of putative alternative splicing information derived from the alignment of proteins, mRNA sequences and expressed sequence tags (ESTs) against human genomic DNA sequences. Proteins, mRNA and ESTs provide valuable evidence that can reveal splice variants of genes. The alternative splicing information in the database can help users investigate the alternative splicing and tissue-specific expression of genes.

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Related in: MedlinePlus

The concept of alignment between protein and genomic sequences to identify candidate exons.
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Figure 6: The concept of alignment between protein and genomic sequences to identify candidate exons.

Mentions: Protein sequences are aligned to genomic sequence in all six possible reading frames by the TBLASTN module of BLAST. The protein-to-DNA alignment is done with the scoring matrix PAM30 and the parameters are extending gap cost 2, opening gap cost 8, and expectation value limitation 0.001. An example of a protein and genomic sequence alignment is shown in Figure 6.


ProSplicer: a database of putative alternative splicing information derived from protein, mRNA and expressed sequence tag sequence data.

Huang HD, Horng JT, Lee CC, Liu BJ - Genome Biol. (2003)

The concept of alignment between protein and genomic sequences to identify candidate exons.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC154580&req=5

Figure 6: The concept of alignment between protein and genomic sequences to identify candidate exons.
Mentions: Protein sequences are aligned to genomic sequence in all six possible reading frames by the TBLASTN module of BLAST. The protein-to-DNA alignment is done with the scoring matrix PAM30 and the parameters are extending gap cost 2, opening gap cost 8, and expectation value limitation 0.001. An example of a protein and genomic sequence alignment is shown in Figure 6.

Bottom Line: ProSplicer is a database of putative alternative splicing information derived from the alignment of proteins, mRNA sequences and expressed sequence tags (ESTs) against human genomic DNA sequences.Proteins, mRNA and ESTs provide valuable evidence that can reveal splice variants of genes.The alternative splicing information in the database can help users investigate the alternative splicing and tissue-specific expression of genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science and Information Engineering, National Central University, Jung-Li City 320, Taiwan.

ABSTRACT
ProSplicer is a database of putative alternative splicing information derived from the alignment of proteins, mRNA sequences and expressed sequence tags (ESTs) against human genomic DNA sequences. Proteins, mRNA and ESTs provide valuable evidence that can reveal splice variants of genes. The alternative splicing information in the database can help users investigate the alternative splicing and tissue-specific expression of genes.

Show MeSH
Related in: MedlinePlus