DNA & PROTEIN SEQUENCE ANALYSIS CONSULTING & SOFTWARE DVMT: BIOINFORMATICS, WWW

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At the Sequence Analysis Consulting Services of UCSF, serving sequence databases and software to over 100 labs including over 1200 people at UCSF, we have the unique advantage of hearing software development priorities directly from the researchers. Areas many scientists feel requires much improvement is user interface and automation. Many bioinformatics programs have yet to take advantage of advances made in areas such as the WWW, Python, Java and the CGI to help improve and simplify the user interface. With the rapid increase in data production through advances in DNA sequencing and DNA micro array technology, there is great interest in developing automated analysis of primary data. Software tools for sequence alignments and structure homology modeling must evolve with the new data produced by efforts such as Genome projects and technologies like DNA arrays. We have designed programs that take advantage of these new technologies to enable the informaticist/scientist to have a more user-friendly and efficient working environment. We have tools in production to help automate the data processing pipeline for primary sequence data and management of these results. We are designing a Perl and Python application for molecular biologists interested in structure to make UNIX sequence analysis and homology modeling tools as easy as browsing the Web. The Computer Graphics Laboratory and its resources offer a unique context for this interdisciplinary work.