Genome Institute of Singapore: GIS / ChIP paired-end ditags

Description

This track shows the start and end sequence tags of mRNA transcripts determined by paired-end ditag (PET) sequencing. PETs are composed of 14-21 bases from either end of a cDNA. See the References section below for more details on PET sequencing. The track shows GIS (gene identification signature) and ChIP (Chromatin Immunoprecipitation) PETs that were pre-processed and fetched with the PET-Tool (Genome Institute of Singapore).

GIS libraries

ChIP libraries

The 5' and 3' ends of the ditag features are represented as small boxes connected by a horizontal arrow indicating the strand/direction. Clicking on the feature brings up a menu with information about this ditag and a link to this more detailed description.

Alignments

The ditags were split in half and aligned to the unmasked genome sequence using Exonerate. The hits were filtered using the following strategy:

Identical sequences and hits to the same location (start & end of ditag) were collapsed into a non-redundant set.

Credits

The GIS-PET & ChIP-PET libraries and sequence data for transcriptome analysis were produced at the Genome Institute of Singapore and processed using their PET-Tool.

The data was mapped and analyzed using code of the EnsEMBL project.

References

Chiu KP, Wong CH, Chen Q, Ariyaratne P, Ooi HS, Wei CL, Sung WK, Ruan Y.
PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data.
BMC Bioinformatics, 2006 Aug 25;7:390.

Ng P, Wei CL, Sung WK, Chiu KP, Lipovich L, Ang CC, Gupta S, Shahab A, Ridwan A, Wong CH, Liu ET, Ruan Y.
Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation.
Nat. Methods 2(2), 105-11 (2005).

Slater GS, Birney E
Automated generation of heuristics for biological sequence comparison.
BMC Bioinformatics 6(1), 31 (2005).