Core Lab Informatics Update

Free sequence data assembly

We use the U. Washington batch processing software (phred, phrap and consed). Besides base calling with quality scores, contig assembly and editing, this suite of programs includes SNP analysis tools.

We also have a license for Sequencher from GeneCodes for fragment assembly and final sequence finishing work.

Local and Remote Blast Searches and Analysis

It's easy to do a BLAST search, but how do you blast 100 or even thousands of sequences, and then extract the results you need? We can help automate your informatics projects. Contact Tom for more information.

EMBOSS Suite of BioInformatics Software

We also have the EMBOSS suite of open source programs installed locally and can use it for various sequence analysis needs.

Primer and Probe Design

We design primers and probes for PCR, sequencing, mutagenesis, SNP analysis, and other applications requiring oligodeoxynucleotides.

We can collaborate on expression verification projects by designing quantitative, real-time PCR probes and primers.

We use the most rigorous and flexible software we are aware of for probe and pcr primer pair design: OLIGO (v.6.0). and Primer3 Data for standard bases, base analogs and labels

Programming & Database Expertise

We have written several custom perl programs for "data-munging" needs within the Core Facility. Data Munging is computerese for parsing a datafile, manipulating or modifying the extracted data and then exporting it in an appropriate format for the next application. We offer this expertise for projects that use our Genomic services. This is usually performed as a collaboration with the expectation of co-authorship on subsequent papers. We can also help in this capacity in support of grants with a genomics component. Recent examples include the orf analysis of the entire Francisella tularensis genome, quantitative real-time PCR primers and TaqMan™ probe design, species specific primer design for qPCR of target cDNA from transgenic animals.

Core Lab Databases

We use Filemaker Pro to "run" the Core Facility. It handles sample, contact, and billing information. We have installed and are developing PostgreSQL database applications.

Please contact Dr. Keller to discuss methods design, data munging needs and troubleshooting experiments. Phone: 503-494-2442.

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