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Smith IDDRC

Bioinformatics Services

We provide a variety of services in bioinformatics and computational biology. Some of these services are listed below. Please feel free to contact the Bioinformatics Core for more information on these services. The Bioinformatics Core will also be happy to discuss with you the feasibility of supporting customer applications specific to your research.
 
High-throughput sequencing
  • RNA-Seq: provides an unbiased deep coverage and base level resolution of the whole transcriptome. Has a low background signal and does not have an upper limit of quantification.
  • Chip-Seq: combines chromatin immunoprecipitation with high-throughput sequencing to provide an unbiased whole genome mapping of the binding sites of DNA-associated proteins.
  • Whole Genome Sequencing: sequences the whole DNA sequence of an organism’s genome.
  • De novo Sequencing: provides the primary genetic sequence of an organism.
  • Metagenomic Sequencing: sequencing and identifying the genomes of whole microbial communities.
  • Methyl-Seq: analysis of methylation patterns on a genome wide scale. 

Microarray analysis

  • Affymetrix 3’ Expression Arrays: target the 3’ end of genes.
  • Affymetrix Exon Arrays: provides expression levels for every known exon in the genome.
  • Affymetrix miRMA Arrays: provides measurements of small non-coding RNA transcripts involved in gene regulation.
  • Affymetrix Genome-Wide Human SNP Array: copy number analysis
  • Affymetrix GeneChip Tiling Arrays: gene regulation analysis 

Biological Functional and Pathway Analysis: we have software from Ingenuity Systems (IPA) that can analyze your expression data to ascertain the top biological functions and pathways associated with them.

Biological Literature Survey: we have software from Acumenta (Literature Lab) that helps perform data mining tasks on experimentally derived gene lists.

miRNA target prediction: we use in house software and open source software such as TargetScan, miRanda for detecting genomic targets for miRNAs.

Transcription Factor Binding Site Prediction: we use in house software and open source software such as MEME, Homer, PGMotifScan to identify protein DNA interaction sites.

 

 

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Supported by the Kansas IDDRC, P30 NICHD HD 002528