It is important visualize more faces to design primer or oligo and PCR experiments:
- calculate thermodynamic parameters of DNA Hybridization (Oligo/Template)
compute hairpin-loop, dimer, bases penality and melting temperature about primer or pair primer
calculate statistics about melting temperature with the change in composition and mix PCR concentration
with google you could find more tools but you must choose a tool of a sequencing team. almost all tools use mfold algorithm, it's simple and effective:
M. Zuker, D. H. Mathews & D. H. Turner. Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide In A Biochemistry and Biotechnology, 11-43, J. Barciszewski and B. F. C. Clark, eds. , NATO ASI Series, Kluwer Academic Publishers, Dordrecht, NL, 1999.
I worked in a sequencing team and there was a programmer. he developed a fantastic tools. he is a little english, but he could support you: http://promix.cribi.unipd.it/cgi-bin/promix/melting/melting_main.exe
Gene Link Downloads
DNA, Probe and Oligo Analysis
1. Oligo Explorer Online:
Oligo Explorer Online helps you to find suitable primer pairs for your purposes. You can set your own parameters for primer pair search engine or use default parameters. Default parameters are usually adequate for most applications. 'Primer wizard' suggests primer pairs that amplify PCR-product of given length. Individual primer pairs have been tested so that they do not form stable primer dimers or primer loops. Copyright of Gene Link, Inc.
Click here to register and access Oligo Explorer Online Version 1.0 BETA
2. Oligo Explorer Software
Oligo Explorer is an efficient easy-to-use tool to determine primer properties like Tm, GC%, primer loops and primer dimers. Oligo Explorer also includes a powerful 'Primer wizard' tool that helps you to find suitable primer pairs for your purposes. You can set your own parameters for primer pair search engine or use default parameters. Default parameters are usually adequate for most applications. 'Primer wizard' suggests primer pairs that amplify PCR-product of given length. Individual primer pairs have been tested so that they do not form stable primer dimers or primer loops. Beta version with TaqMan and Molecular Beacon probe analysis features not completely implemented. Copyright of Gene Link, Inc.
Click here to register and download Oligo Explorer Version 1.5 BETA
3. Gene Runner:
An old but robust DNA analysis application. This was a commercial product initially and is now �abandonware� and available for free download. The oligo analysis feature especially for stem and loop formation is particularly useful. Copyright of Hastings Software Inc.
Click here to download Gene Runner Zip Archive
Sequencing Electropherograms Editing Applications
Gene Link provides the electropherogram (chromatogram) files of the sequencing run. We recommend that the investigator verify the edited sequence data provided by Gene Link. There are shareware and free applications available for viewing, editing and printing chromatogram files.
1) FinchTV for Windows/MAC/Solaris/Linux:
Geospiza's FinchTV is the popular way to view DNA sequence traces on Linux, Mac OSX, Windows, and Solaris. FinchTV started as the only chromatogram viewer that can display an entire trace in a scalable multipane view. Now it leads again with raw data views, BLAST searching and the ability to reverse complement sequences and traces.
2) Chromas for Windows:
Chromas is a Windows application that displays and prints electropherogram files from ABI automated DNA sequencers and most other DNA sequencers. It is a PC shareware free for 6 months and limited use capability after 6 months. Chromas Download Information
3) EditView for Macintosh:
EditView is a software application that allows you to view and print analyzed sample files containing sequence data from ABI DNA sequencers. EditView Download Information