Roadrunner Genomics Laboratories is the nonprofit core genome sequencing laboratory and associated bioinformatics
facilites of New Mexico State University as part of the Biology department
We offer:
- De novo shotgun, amplicon and paired-end sequencing
- Transcriptome sequencing and analysis
- Custom data management and analysis pipeline
- Microsatellite markers development
and in silico genotyping
- Phylogenomics and DNA resequencing
- Genome browser based web-interface and FTP
From custom GBrowse displays to developing transcriptome and in silico genotyping analysis tools, our services end at the desired level of completion.
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Unmatched speed and project support
Sequencing beyond A’s, C’s, G’s, and T’s
Roadrunner Genomics Labs at New Mexico State University offers Roche 454 GS-FLX sequencing and bioinformatic services. Innovative analyses and visualization are presented to investigators through our Genome Browser graphical web-interface along with conventional FTP access.
Genome browser
We offer our clients more than nucleotides; rather, we aim to assist your project toward completion. Harnessing the facility’s 16 node compute cluster, database and web servers, projects are accessible throughour web-interface, Genome Browser. Genome Browser displays GC-content, read density and depth of coverage for your project data as just the beginning toward understanding your results. Offering each client web-accessible securely protected results in our appealing Genome Browser as standard service; we intend to deliver you data in a useable format.
Variant detection
Comparative sequencing projects greatly benefit from the 454 GS-FLX sequencing capabilities and our variant detection displays within Genome Browser. To focus on biologically relevant polymorphisms in your project, Genome Browser automatically displays polymorphic sites as synonymous and non-synonymous substitution variants.
Transcriptome analysis
Benefitting from 500 bp reads and in-house bioinformatic applications, we offer advantageous support for transcriptome sequencing projects. Whether you are interested in detecting isoforms, alternative splice sites, or variation in genomic expression levels, we provide unmatched bioinformatic support with each project.
Microsatellite discovery and in silico genotyping
We offer an array of support for population genetic projects. From microsatellite discovery to simultaneous discovery and genotyping, we can assist your search for polymorphic markers. Combined with 454 multiplex capabilities, read numbers and length, our microsatellite services offer unique support for population-level studies. This type of analysis benefits from longer reads available with 454 GS-FLX platform, which allows locus assignment and simultaneous allele classifivation for the raw reads originating from a Simple Sequence Repeats (SSRs) enriched genomic DNA library.
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Recent presentations
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Screenshots of completed projects
You will need to have Adobe Reader
installed on your machine to view the high-resolution screenshots.
Cryphonectria parasitica variants detection and analysis
Example of reads from SSRs enriched library, originally composed of genomic DNA fragments digested with MSEI restriction enzyme.
New Mexico outbreak Mycobacterium bovis strain variants detection and analysis
This particular 4.5 MBp strain genome was severely oversequenced by loading sample to the whole plate,
which is not always necessary. In this case coverage of sligtly more than 15x (half plate) would be sufficient
for high quality contigs assembly and 7x (quarter plate) would be sufficient for reliable variants calling with
gsMapper software (Roche). We can arrange only portion of the plate to your individual project either
using Miltiplex Identifiers (MIDs) or by physical samples separation with the gasket as explained
here.
Aedes aegypti (yellow fever mosquito) transcriptome analysis
One read spans across 5 exons which demonstrates advantage of having 454 GS-FLX longer reads.
Illumina cow transcriptome reads
The immune response transcriptome has been sequenced at NCGR.
Although most of the splice sites have been resolved, Illumina coverage is very uneven.
This analysis demonstrates our capabilities of exploring Illimina runs.
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Recent media
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Contact information
- MSC 3AF, Foster Hall
- 1200 S. Horseshoe Dr.
- New Mexico State University
- Las Cruces, NM 88001
- Phone 575-646-7980
- Fax 575-646-5665
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Roadrunner Genomics Laboratories is the
NSF-supported nonprofit core genome sequencing laboratory and associated
bioinformatics facilites of New Mexico State University as part of the
Biology department. This work was supported in part by
NSF award # DBI-0821806 to P. Houde.
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