arkerlav@HELIX.NIH.GOV (Anthony R. Kerlavage) (02/10/90)
In response to your question to human-genome-program: Most people are using shotgun cloning for sequencing projects. As projects become larger this method will probably continue to be the most widely used. The ability to do primer walking to fill in gaps will make this method extremely useful. Other approaches may become more widely used, such as ordered deletions and gene walking. Our laboratory uses automated sequencing techniques and the average readable sequence is on the order of 500 bases. The most commonly used tools for sequence assembly are the Staden, Wisconsin (GCG), MBIR (Baylor), and IntelliGenetics packages. Several packages are also available for PCs or Macs, but will probably not be suitable for very large projects. It is generally agreed that none of the currently available software is adequate for very large (>10,000 bases) projects. New approaches (both hardware and software) are in the works but may not be available for some time. I encourage you to contact me by phone (301/496-8800) if you would like to discuss any of these issues in more detail, since they are too complex to cover here.