Copyright (C) 2000 Karl T. Diedrich
Published by Karl T. Diedrich
The DEODAS manual is available from the DEODAS web site
http://deodas.sourceforge.net/
Permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and this permission notice are preserved on all copies. Permission is granted to copy and distribute modified versions of this manual under the conditions for verbatim copying, provided also that the sections entitled "Copying" and "GNU General Public License" are included exactly as in the original, and provided that the entire resulting derived work is distributed under the terms of a permission notice identical to this one. Permission is granted to copy and distribute translations of this manual into another language, under the above conditions for modified versions, except that this permission notice may be stated in a translation approved by the Free Software Foundation.
A GNU/Linux-based system, called the DEgenerate Oligonucleotide Design & Analysis System (DEODAS), for designing and electronically analyzing consensus-degenerate oligonucleotides is being developed by integrating published software tools Clustalw, CODEHOP, and EMBOSS (see section References). DEODAS also adds new functionality to oligonucelotide design. Related protein sequences are input into the system. Clustalw produces multiple sequence alignments and phylogenetic tree files. Subgroups are formed based on the phylogenetic tree. The subgroups are realigned and degenerate oligonucleotides are produced by CODEHOP. The oligonucleotides are screened against Genbank sequence databases by fuzznuc from EMBOSS. DEODAS integrates these software tools to automate the design and screening of oligonucleotides in batch. This greatly decreases the amount of interactive time required to design and screen probes. Output detailing the designed oligonucleotides is organized in searchable databases that are used to examine and select probes and PCR primers for synthesis and laboratory testing.
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