Genetic Tools

1. Hyper PCR The hypercard stack is used to determine the optimal annealing temperature for PCR. Developed by Brian Osborne.
   • The stack is designed to work on any Macintosh equipped with Hyper Card v.2.0 or Hyper Card Player. In order to start the application from your Web browser, the new Mime type "application" with the subtype "hypercard" (application/hypercard) must be added to the Helper Applications list in the Web browser. Select the copy of HyperCard that will launch this type of document. Set the document file type to "STAK" and the file extension to "hc".
   • If you are using NCSA Mosaic 2.0 alfa: 1) Open the Options menu, select "Preferences," click on "Apps" icon and then on "Helper Application" button. 2) Click on "Add document type" button and type "application/hypercard" in window. Click "OK." 3) Press "Set Application" button, select your copy of Hypercard and pick a file type as "STAK." 4) Click on "Add extension," type "hc" in the "Extension" window and set Mime Type to the new item - "application/hypercard." Click "OK" and then "Apply".
   • For Mosaic Netscape users: 1) Open "Preferences" in the "Option" menu and select "Helper Application" in the top window. 2) Press the "New" button. Enter "application" as the Mime type and "hypercard" as the Mime subtype. Click "OK." Enter "hc" in the "Extensions" field. 3) Click on "Browse" and find "HyperCard" on your hard disk. Select "HyperCard" and click "Open". 4) Click on the "Launch application" radio button in the "Action" menu. 5) Highlight "STAK" in the "File type" window and drag mouse down to "OK" in order to save your new options. Be sure to set file type as "STAK" at the end of the installation. If the HyperCard doesn't open HyperPCR stack and shows the "Home" page only, check the file type again and reset it to "STAK."

2. Tm - Oligonucleotide Melting Point Determination at U. Minnesota

3. Poland - Calculate the Thermal Denaturation Profile of Double Stranded RNA or DNA at Uni-Düsseldorf, Germany

4. STS Pipeline at MIT. Performs duplicate checking, simple sequence repeat finding, vector identification, BLAST searching, and the actual primer picking itself.

5. Primer 2.2 Primer design. WWW Front End.

6. Primer A Primer Design Tool at the U. Minnesota

7. MSA - Multiple Sequence Alignment at Washington U.

8. Multiple Sequence Alignments - CLUSTAL-W, MAP, and PIMA alignments at Baylor College of Medicine

9. CLUSTALW - Multiply Sequence Alignments at IBC-Washington U.

10. LALIGN - Calculates the N-Best Local Alignments Between Two Sequences at EERIE-Nimes, France

11. ALIGN - Optimal Global Alignment of Two Sequences with No Short-cuts at EERIE-Nimes, France

12. Align at MIPS, Germany

13. Basic Local Alignment Search Tool - BLAST
    • At the Japan Genome Center
    • At the NCBI
    • At Stanford U.
    • BLAST at EPFL, Switzerland
    • BLAST at CRIHAN, France
    • BEAUTY - BLAST Enhanced Alignment Utility at Baylor College of Medicine

14. BOXSHADE - Pretty Printing and Shading of Multiple-Sequence Alignments at ISREC, Switzerland

15. WebLogo - Sequence Logo Generation at Cambridge U., UK

16. MOTIF - Searching protein sequence motifs

17. PMOTIF - Search Protein Motifs in Gene Sequence at U. Minnesota

18. Sequence Translation - Translate Gene Sequences at U. Minnesota
19. Translate - Translate a Nucleotide Sequence to a Protein at ExPASy, Switzerland
20. PSORT - Prediction of protein Sorting Signals

21. FASTA - Compare a Nucleic Acid Sequence to Nucleotide Sequence Databases at EBI, UK

22. FASTA (Berlin, Vectorbank, etc) at Stanford U.

23. FASTA at EERIE-Nimes, France

24. FASTA at CRIHAN, France

25. TFASTA - Match a Protein Sequence Against All Six Frames of GenBank Sequences at EERIE-Nimes, France

26. PatScan - Look for Pattern Matches in DNA or Protein Sequences at Argonne National Laboratory

27. ProfileScan - Search a Sequence Against a Library of Profiles at ISREC, Switzerland

28. RSVP - Rapid Sequence Visualization in Postscript for Analysis of DNA Sequences at CBIL-U. Pennsylvania

29. Sequence Translation - Translate Gene Sequences at U. Minnesota

30. Translate - Translate a Nucleotide Sequence to a Protein at ExPASy, Switzerland

31. SSEARCH - Universal Sequence Comparison Using the Smith-Waterman Algorithm at EERIE-Nimes, France

32. BioSCAN - Biological Sequence Comparative Analysis at U. North Caroline
33. Dot Plot - Compare a DNA Sequence with Itself at U. Minnesota
34. Grail - Analysis of the Protein Coding Potential of a DNA Sequence at ORNL
35. PHILIP-Bootstrapping Analysis - Divergence Between Protein or Nucleotide Sequences at Institut Pasteur, France
36. GenLang - Find Genes and Other Higher-Order Features in Nucleotide Sequences at CBIL - U. Pennsylvania

37. Codon Usage - Analysis of Different ORFs in a Gene Sequence at U. Minnesota

38. Gene Finder - Predict Gene Structure, Internal Exons and Splicing Sites in DNA and Exon-Exon Junction in cDNA at Baylor College of Medicine

39. EMP Metabolic Pathways - Navigation in Metabolic Pathways from MCS-Computational Biology at Argonne National Laboratory

40. Pedro's BioMolecular Research Tools A Collection of WWW Links to information and Services Useful to Molecular Biologists.

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