This chapter answers some frequently asked questions about the DNAMAN program.
Answer: Read the section II.3 and II.4 of this document to understand DNAMAN and get started with the program.
Answer: You should load the sequence into a channel in order to analyze it. Chapter III of this document describes the basics of DNAMAN.
Answer: In theory, DNAMAN can handle sequences up to 2 giga-bases (2x109). The limitation is the computer resources. It takes a lot of memory and computing power to handle such a long sequence. We have tested the program with sequences of several mega-bases. The functions of multiple alignment and sequence assembly have different limitations in sequence input.
Answer: You may use up to 32000 sequences with a maximum length of 64000 bases. Again, the limitation is the computer power. It may be really slow with long sequences. We have tested the program with 1000 sequences of approximately 300 amino acids.
Answer: You may use up to 32000 DNA fragments with a maximum length of one giga-bases. Again, the limitation is the computer power. It may be really slow with long sequences. We have tested the program with 2000 sequences of approximately 300 bases.
Answer: Yes, you may. You may prepare DNA maps, cloning strategies and other graphics with DNAMAN. These maps can be enlarged and printed out in several pages.
Answer: Yes, you may. Use the File | Run menu to launch a program. You have the option to display the results in the DNAMAN studio.
Answer: The DNAMAN browser is designed to browser the databases on the Internet, or your Intranet. You have an option to use your favorite browser by choosing the Info | Settings menu.
Answer: A multiple threaded function runs in its own thread. It will not block a program to run other modules. If a function is not multiple threaded, users must wait for the end of the function in order to start a new function. With a multiple threaded function, users may start other functions immediately. Multiple threaded functions utilize better multiple-processor computers. The multiple alignment of DNAMAN is multiple threaded. You may launch up to 16 processes of multiple alignment running in the same time. The sequence assembly function is also multiple threaded. Producing trees from multiple alignment falls also into this category.