Description

This track shows the graphs constructed by analyzing experimental RNA transcripts and serves as basis for the predicted alternative splicing transcripts shown in the SIB Genes track. The blocks represent exons; lines indicate introns. The graphical display is drawn such that no exons overlap, making alternative events easier to view when the track is in full display mode and the resolution is set to approximately gene-level.

Further information on the graphs can be found on the Transcriptome Web interface.

Methods

The splicing graphs were generated using a multi-step pipeline:

1. RefSeq and GenBank RNAs and ESTs are aligned to the genome with SIBsim4, keeping only the best alignments for each RNA.
2. Alignments are broken up at non-intronic gaps, with small isolated fragments thrown out.
3. A splicing graph is created for each set of overlapping alignments. This graph has an edge for each exon or intron, and a vertex for each splice site, start, and end. Each RNA that contributes to an edge is kept as evidence for that edge.
4. Graphs consisting solely of unspliced ESTs are discarded.

Credits

The SIB Alternative Splicing Graphs track was produced on the Vital-IT high-performance computing platform using a computational pipeline developed by Christian Iseli with help from colleagues at the Ludwig Institute for Cancer Research and the Swiss Institute of Bioinformatics. It is based on data from NCBI RefSeq and GenBank/EMBL. Our thanks to the people running these databases and to the scientists worldwide who have made contributions to them.