Bioinformatics and Software

Contig Assembly and Sequence Inspection Using phred, phrap, and consed

The freely available (for academic users) phred base caller and phrap contig assembler are the de facto standard used by the majority of sequencing centers. Consed then allows to inspect, edit and export contigs and individual traces, and much more. A setup that worked well in my previous lab was to have phred/phrap/consed installed on an old PC running Linux, and lab users then accessed the programs using SSH and an X-server from their Win or Mac computers. Go to http://www.phrap.org for license agreement, download and user manual. View the instructions how to run the software remotely from your PC: using_consed_ssh.pdf

How to Set Up Blast2 in the Bioedit Freeware

Bioedit is an excellent, freely available (http://www.mbio.ncsu.edu/BioEdit/BioEdit.html) sequence alignment editor with many neat features, including the ability to run local Blast searches and to call external application. To set up an accessory application to blast two sequence against each other, follow this procedure: blast2_Bioedit.pdf

Using "tacg" Restriction Analysis Program With Bioedit

While Bioedit has a built-in restriction analysis feature, some people prefer the "tacg" program because of its output format and versatility. Follow these instructions to install. Please note that tacg is a unix program. To run it on your PC, you will need a Cygwin basic package and a Cygwin-compatible version of tacg. View the instructions:  tacg_Bioedit.pdf