Orphan gene finding—an exon assembly approach

On the Complexity of Sparse Exon Assembly

Gene structure prediction is one of the most important problems in computational molecular biology. It involves two steps: the first is finding the evidence (e.g., predicting splice sites) and the second is interpreting the evidence, that is, trying to determine the whole gene structure by assembling its pieces. In this paper, we suggest a combinatorial solution to the second step, which is als...

Faster exon assembly by sparse spliced alignment

Assembling a gene from candidate exons is an important problem in computational biology. Among the most successful approaches to this problem is spliced alignment, proposed by Gelfand et al., which scores different candidate exon chains within a DNA sequence of length m by comparing them to a known related gene sequence of length n, m = Θ(n). Gelfand et al. gave an algorithm for spliced alignme...

Assembly and mobility of exon-exon junction complexes in living cells.

The exon-exon junction complex (EJC) forms via association of proteins during splicing of mRNA in a defined manner. Its organization provides a link between biogenesis, nuclear export, and translation of the transcripts. The EJC proteins accumulate in nuclear speckles alongside most other splicing-related factors. We followed the establishment of the EJC on mRNA by investigating the mobility an...

Rapid Assembly of Multiple-Exon cDNA Directly from Genomic DNA

BACKGROUND Polymerase chain reaction (PCR) is extensively applied in gene cloning. But due to the existence of introns, low copy number of particular genes and high complexity of the eukaryotic genome, it is usually impossible to amplify and clone a gene as a full-length sequence directly from the genome by ordinary PCR based techniques. Cloning of cDNA instead of genomic DNA involves multiple ...

CWC22 Supports Pre-mRNA Splicing and Exon Junction Complex Assembly