We will continue to develop software environments for solving two computational problems in molecular biology. The first problem is sequence alignment; the second is integrating sequence data, physical maps, and genetic maps. In each case, development of an appropriate software environment involves (1) designing and implementing algorithms, (2) constructing a graphical user interface, (3) building tools to print publication-quality graphical output, and (4) designing and constructing software to handle heterogeneous and interrelated sets of data. The software that we develop is implemented in a reasonably portable manner and is distributed free of charge. Our current software environment for sequence alignment will be enhanced to handle alignment of more than two sequences and to compute and display information about the trustworthiness or robustness of the alignments. Tools to extract information, such as the presence of coding regions, from alignments will be built. Better mechanisms for interactively recording and displaying sequence features will be developed, and a hypertext system will be designed and built for managing the resulting corrections of sequences, sequence features, and alignments. Additional alignment algorithms that strike a balance between sensitivity and efficiency will be developed and tested. Finally, if given funds for the task, we will integrate the software environment with the Software Development Kit from the National Center for Biotechnology Information to make the environment available on a wide variety of computers. Our current software environment for integrating sequence data, physical maps, and genetic maps will be given a comprehensive graphical user interface and the complex data-management questions will be addressed. We will also develop algorithms to search a genomic restriction map with fragment-length data and will continue work on algorithms to search and to compare restriction maps.
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