98. Mapping Data 

Lixin Tang, Jeremy Boulton¹, Benjamin Liau¹, Hui Zhang², Wei Qin³, Sung Ha Huh¹, Yicheng Cao, Robert Xuequn Xu, Glen George¹, and Ung-Jin Kim 
Division of Biology, ¹Computer Science, ²Atmospheric Chemistry, and ³Electrical Engineering, California Institute of Technology, Pasadena, CA 91125 
xux@cco.caltech.edu 

In building the physical contig maps of human and other chromosomes, we found that a high degree of automation as well as a high degree of flexibility is usually desired at the same time. Despite remarkable progresses in physical mapping projects and biocomputing, a computer software tool that allows both is not yet available albeit there are some mapping tools that heavily rely on automation and allow limited human intervention. 

AceDraw is a graphical software tool that we have developed in order to facilitate drawing, updating, and database entry of physical mapping data. It is capable of reading the content of ACeDB database, allows graphic display and freehand editing of the physical maps, and dumps the physical map in a file that can be parsed by ACeDB. The program was written in C++ and used a freely available relational database, MySQL, as a backend. It helps to manage the mapping data in a way that can be organized and viewed in which the location and order of clones and landmarks and overlaps between clones are displayed along the length of chromosomal regions. It is similar to ACeDB in this respect, and it can actually take in the ".ace" files and draw more presentable and intuitive contig maps using a large number of colors, with each assigned color associated with certain traits of associated data, such as "sequenced", "fingerprinted", and/or "end sequenced", etc. It can save the mapping data back into ACEDB format after drawing, modification, and updating, thus allowing using of the special functionalities provided in ACEDB. 

An important feature of AceDraw is that it is a freehand drawing tool that enables easy human intervention to resolve conflicts in the contig map by direct manipulations on clones and markers such as clone searching, moving, resizing and color changing. AceDraw also allows easy creation, modification and deletion of clones and landmarkers without low-level editing of database files, and thus facilitates map construction. Since AceDraw is associated with relational database model, querying the database for an object of interest can be done easily. Moreover, AceDraw supports map output into high resolution postscript files for the printing of hardcopy maps.