Transcription initiation occurs from a specific site on each chromosome with 'polycistronic' RNA intermediates that are in turn trans-spliced and polyadenylated based on splice site recognition [31] [33].
Finally, we also investigated the role of selection on splicing site recognition.
Besides, the possible effects of predicted conformational flexibility and disorder on sumoylation site recognition were explored computationally for the first time to our knowledge as an additional parameter that could aid in sumoylation site prediction.
A number of assays have been developed to confirm direct effects of variants on splice site recognition, however fewer methods are available to measure effects of mutations at binding sites of splicing regulatory proteins.
Most investigations of the effect of genetic variation on miRNAs have so far been focused on genetic influence (e.g., 3′ UTR SNPs) on miRNA target site recognition.
Systematic modification of the structure of the photoreagent provides valuable information on the binding site recognition as well as the mechanism of the photocleavage reaction.
In recent years, SVMs have been widely used in life sciences research, such as for studies on alternative splice site recognition, biomarker selection, remote homology detection, gene function prediction, and protein protein interaction prediction, among others (Pavlidis et al. 2002; Liao and Noble 2003; Ben-Hur and Noble 2005; Ratsch et al. 2005; Sonnenburg et al. 2007).
To test whether TIA1/TIAL1- or HNRNPF/H-binding sites downstream of this 5′ splice site can restore its recognition, we inserted two copies of each binding site into the downstream intronic flank (fig. 8 B) and analyzed their impact on 5′ splice site recognition.
In addition, we are planning to develop a stand-alone implement with parallel computation option for Drosha processing site recognition on different OS platforms.
We developed a suite of methods for the problem of protein binding site recognition, based on a representation of the protein structures by a collection of spin-images.
