Browsing by Author "Jimenez, Rafael."

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Vector graphics to improve BLAST graphic representations
(2007) Jimenez, Rafael.
BLAST reports can be complicated. Viewing them graphically helps to understand them better, especially when the reports are long. At present "Web BLAST" and the stand-alone "wwwBLAST" versions, distributed by the NCBI, include graph- ical viewers for BLAST results. An alternative approach is "BLAST Graphic Viewer" developed by GMOD as part of the BioPerl library. It provides a more aesthetically pleasing and informative graphical visualization to represent BLAST results. All the strategies mentioned above are based on the use of bitmap graph- ics and dependent on JavaScript code embedded in HTML. We present Vector Graphic BLAST (VEGRA) a Python object orientated library based on BioPy- thon to yield graphical visualization of results from BLAST utilizing vector graph- ics. Graphics produced by VEGRA are better than bitmaps for illustration, more exible because they can be resized and stretched, require less memory, and their interactivity is more e ective as it is independent of tertiary technologies due to its integration into the graphic. In addition, the library facilitates a de nition of any layout for the di erent components of the graphic, as well as adjustment of size and colour properties. This dissertation studies previous alternatives and improves them by making use of vector graphics and thus allowing more e ective presentation of results. VEGRA is not just an improvement for BLAST visualiza- tion but a model that illustrates how other visualization tools could make use of vector graphics. VEGRA currently works with BLAST, nevertheless the library has been written to be extended to other visualization problems.