Our particular specialty is in the assembly, annotation, and analysis of bacterial genomes from a variety of platforms. These services are provided by our bioinformatic experts and collaborators at the University of Nebraska. De novo sequence data can be generated using Roche 454, Illumina/Solexa, ABI SOLiD, or Sanger sequencing platforms by UNMC's DNA Microarray Core Facility, High-Throughput DNA Sequence Core Facility, or other campus collaborators for verification of the results obtained.
Specialized and specific software can be developed by our bioinformatic group to meet the needs of the project. We also employ state of the art optical mapping of genomes by OpGen using defined restriction endonucleases. This technology provides a contiguous alignment of chromosomal fragments, facilitating and expediting the assembly of DNA sequences and/or contigs.
Other traditional and next generation nucleic acid services available for the acquisition of biological information include:
- Genomic re-sequencing with variation analysis and annotation
- De novo genome assembly, gap closure, and annotation
- Metagenomic analyses
- Genetic profiling (e.g. 16S or 23S rRNA, RAPD, MLST, AFLP, and PFGE)
- Gene, transcript, and promoter identification
- Annotations for gene characterization and ontology comparisons to find conserved synteny
- RNA sequence analysis for gene expression, e.g. microarray gene expression/characterization or transcriptome applications
- Targeted sequence capture and variation analysis such as the identification of single-nucleotide polymorphisms (SNPs)
- Chromatin immunoprecipitation (ChIP) sequence analysis to determine the location of DNA-binding proteins on the genome for a protein of interest
- RNA immunoprecipitation (RIP) sequence analysis to identify protein-RNA interactions
- Primer designing for preferred specificity along with the associated biophysical details for PCR-based applications
- Plasmid, BACs, cosmids, fosmids, and lambda phage library analyses
Visualization of publication quality data that can be displayed in different formats such as histograms, dendrograms, maps, arrows, and/or graphs with coordinates. These various formats include:
- Linear or circular map illustrations
- Multiple sequence alignments to compare gene structure in different organisms to determine relationships and biological functionality
- Displays of gene expression levels
- Illustrations of assembled contigs to show coverage
- Statistical comparisons and analyses
Our department strives to meet the needs of the scientific community for all aspects of biological research to advance science and health. Querying the data at many levels and providing high quality, reliable genome-based information in a timely manner is of paramount importance. The accessibility of data mining tools and genome/sequence browsers through projects by the National Center for Biotechnology Information (NCBI), University of California, Santa Cruz (UCSC) Genome Bioinformatics, DNA Data Bank of Japan (DDBJ), and Ensembl (a joint project between European Molecular Biology Laboratory and Sanger Centre) provide additional and excellent resources for sequence analyses, as well as current and publically available genomic information. As cutting-edge technology and third generation tools are created and proven successful, these resources are added to the already large repertoire of genome acquisition, assembly, and analysis services available.