OHSU

Bio-informatics

Data Processing & Database Development

We offer free sequence assembly and primer design.

We can also help with database development, data processing & automation programming (aka "Data Munging") and batch processing. On-going projects can be either collaborative or fee-for-service.

If you find yourself cutting and pasting lots of data, or searching through long blast or other reports by hand, I can write scripts to automate the process and generate a spreadsheet or set of database records with the extracted bits.

Email Tom Keller, PhD
or phone: 503-494-2442.

Open Source and Free Tools

DNA Sequencing Data: Viewing & Editing

Apple OS X
4Peaks, FinchTV         
Linux FinchTV
Windows XP or 2000
Sequence Scanner, FinchTV

Fragment Analysis: Viewing & Editing

Apple OS X
suggestions?
Linux suggestions?
Windows XP or 2000
Peak Scanner

Alignment & Assembly

Specialized BLAST -- Align two (or more) sequences (bl2seq).

For gene sequencing projects, we use the University of Washington (free for academic use) programs: phred, phrap, consed (shown above) and polyphred (SNP calls). The figure below shows a set of aligned reads. It's the industry standard, but takes some system administration expertise to get running.

An easy to install, cross-platform application is ClustalX (gui for clustalw). It is available on-line too. For Unix (and Unix-like, e.g. MacOSX), there are T-Coffee and MAFFT (cross-platform) These are available for use on-line as well.

consed_polyphred
Sequence Assembly - SNP Detection - BLAST Analysis