Multiple Analysis Resources
for Prokaryotic Sequences.

The Analysis Engine provides multiple analysis resources for prokaryotic sequences. These are listed below. We are also happy to talk with you about any custom analysis needs that you have. Most of our services are offered two ways: fee-for-service or users can access and run the pipelines independently. Links and more information are provided below. If you have questions or wish to talk to us about a custom analysis project, please contact us to tell us about your needs.

Whole Genome Annotation

We have developed two pipelines that provide automated structural and functional annotation of prokaryotic genomes. Both pipelines use Prodigal for gene finding, followed by searches on the predicted protein sequences using multiple tools, and finally annotations assigned based on an evidence hierarchy such that the highest ranking evidence is used to provide annotation for each protein.

Whole Gene Annotation
Comparative Genomics

Comparative Genomics

The Analysis Engine offers two different methods for doing comparative analysis of prokaryotic genomes. Both methods employ the tool Sybil to visualize results.

Transcriptome Analysis

The prokaryotic transcriptome analysis pipeline at IGS is a comprehensive resource that provides several of the most common transcriptomic analysis tasks. The first step in the analysis is alignment of RNA-Seq reads to a reference genome resulting in BAM files. Using the BAM files for each sample, the RPKM (reads per kilobase per million mapped reads) values for each gene in the samples is calculated based on the gene annotation contained in the reference genome. In order to identify genes that have increased or decreased expression in one set of samples vs. another, differential expression analysis is performed using DEseq and EdgeR on the read counts generated using HTSeq. The results for the sample comparisons are filtered and the output stored in tab-delimited text files as well as Excel spreadsheets. Read more.

Transcriptome Analysis

Genome Assembly

To run this independently use the CloVR Microbe resource. Assembly is included when using our fee-for-service sequencing center to generate genome sequence. Contact us for more information.

Custom Analysis

If you have analysis needs beyond what is outlined above, please check out our services page and contact us to discuss the needs of your project. We can provide custom analyses (for both prokaryotes and eukaryotes) on a fee-for-service basis.

List of publications where the Analysis Engine was used.


We offer several training workshops each year that focus on a range of omics approaches and bioinformatics applications.

Please visit our workshop page for more information.


We gratefully acknowledge the National Institute of General Medical Sciences for funding earlier versions of this service.