The Online Artificial Gene Design discussion on Slashdot produced several suggestions for software that can help in design and analysis of DNA sequences, in addition to the Gene Design suite that started the discussion. Unfortunately, only one of the suggested resources – Sequence Manipulation Suite – has a significant number of DNA analysis tools that may be useful for oligonucleotides.
The rest of the resources are related to genomics as well as protein design, expression, and analysis.
NCBI – National Center for Biotechnology Information – offers a collection of links to software and resources for molecular biology.
EMBL-EBI – European Bioinformatics Institute at the European Molecular Biology Laboratory – offers another collection of software.
PlasMapper “automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input”.
New England Biolabs site has a few useful resources in the technical reference section.
ExPASy Expert Protein Analysis System “is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE”.
EMBOSS – The European Molecular Biology Open Software Suite, for *nix machines only; GUI and browser interfaces available.
BioPerl language for bioinformatics.