Penn Genomics Analysis Core

Sequence Analysis/Database Searches

Sequence Assembly & Analysis

Assembly of sequences into a contig, identification of ORFs, analysis of properties of the predicted protein, and other analyses can be performed at the facility using MacVector, Sequencher and other software.

These services are included at no charge for large sequencing projects. Training on the use of MacVector and Sequencher is provided free to the investigators.

The network licenses of MacVector, Sequencher and other desktop software are available from the Bioinformatics group of the Penn Molecular Profiling Facility.

Database Searches

BLAST, BLOCKS, BLITZ, PROSITE and FASTA searches are performed using WWW or e-mail servers at no charge. Please contact the facility to arrange for database searches or for training. Genomic sequences can also be processed to identify interspersed repeats, low complexity regions, GRAIL exons, transcription factor binding sites, frequency of mono, di, and tri nucleotides, and other features. Genomic sequences can also be submitted to the GAIA genome annotation system at the Bioinformatics Laboratory. Facility staff will also submit sequences to Genebank if requested by the investigator.

Penn Genomics Analysis Core is an Abramson Cancer Center Shared Resource that is approved and partially funded by the National Cancer Institute.


Collection boxes have now been put in the lobby of BRB next to the UPS box and the 1st floor lobby of TRC (near the FEDEX box at the back).  Samples for DNA (Sanger) sequencing can be dropped off into the boxes.  Submission instructions and more information here.

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