ProbePicker / News: Recent posts

New version 0.6 is available. It fixes some bugs of the previous version, but has a very minor bug of printing verion 0.51 when it should be 0.6. I don't feel like changing it becuase the issue is minor, if you need the correct version printed contact me and I will send you the correct version printing code.

Featurama is now integrated with BLAST in a new project http://biosap.sourceforge.net . It includes a robot (daemon) program that runs the biosap pipeline automatically on parameter files placed in subdirectories of a specified root directory. The output is a simple XML document the dtd for which is provided. The features generated can be evaluated for potential cross-hybridization by looking at the output directly, or by importing the XML into a database and searching to database.

Featurama is being integrated into a new package called BioSap. Please visit the http://sourceforge.net/projects/biosap/ site for info. We will do a cvs dump as soon as the tools for parsing the xml output into a database are completed (hopefully early in the first week in October).

After noticing that people were downloading ProbePicker we have made the ProbePicker package hidden. We will now only be supporting the Featurama package whose functionality goes above and beyond ProbePicker.

Version 0.3 shows significant speed increases over previous versions and over ProbePicker; where v0.2 took days to select unambiguous oligo's for the 6312 gene yeast set, it now takes between 30 seconds and 6 minutes.

Processing speed on this gene set scales linearly with the speed of the processor. We are beginning to think about ways to parallelize the program.

Running blast still takes an hour or two, however review of the blast results on oligos selected shows that oligo's selected have homology only to the genes intended, so blast may not be necessary in the long run, at least not for yeast.... read more

ProbePicker is now known as featurama and instead of being perl code, it is being written in C++.

ProbePicker is being superceded by Featurama. Featurama is being written in C++ with better memory management for use with larger datasets.

It will incorporate more parameters for probe selection, including heuristics similar to affymetrix. The size of each step through a gene is user definable.

Featurama should be much faster and select better probes. It will output data in XML format so it can be more easily input into a user defined database.... read more