Changes in Oligo 7 Updates up to Version 7.10. Adding functionality to the search for TaqMan PCR primers: you may initiate search for PCR primers compatible with already selected Upper or Lower Probe. Updates up to Version 7.19. New functionalities added: -In the Database multiplexing of the entire primer/probe sets was introduced. -Enabling analysis of the large sequence files: if a sequence file is larger than 250kb Oligo asks which 250 kb fragment needs to be analyzed. This 250kb threshold can be changed by the user. Increasing file size to 1M or larger is possible, but all calculations take a long time and it is not recommended. -Upgrading the Installer. Oligo searches automatically for the available updates (a feature that can be turned off in the Preferences). -Version 7.20. New functionality added: Possibility of probes multiplexing in the Database. Up to this version, only the primers were multiplexable. This version checks for (inverse) homology of probes that determines their self- and cross-hybridization propensity as well. -Version 7.21. New functionalities added: Search for TaqMan probes with already pre-selected PCR primers. Also (for Mac only) made it compatible with the most recent Java (older versions were loosing menu bars with the newest Java update). -Version 7.22. Search for TaqMan probes was optimized. -Version 7.23. Making more descriptive registration screen. -Version 7.24. Fixed a bug causing the Help menu to be less functional than intended. Also fixed (Mac Version) a bug causing some windows to be non-closeable. -Version 7.25 and 7.26. Some minor bugs were fixed. The main included program hanging after changing certain File-Print Options. -Version 7.27. New functionality added: A new column has been added to the Database sets table: it displays the size of the PCR product. -Version 7.28. New functionality added: The Search Ranges Dialog has new item that allows finding only one overlapping PCR primer. -Version 7.29. Fixed a bug in the search for TaqMan Probes introduced in v. 7.28. -Version 7.30, 7.31. Improved search algorithm for TaqMan probes. -Version 7.32. Changed some defaults, such as automtic alignment in Edit window and Tm threshold for hybridization probes search. -Version 7.33. Changed a method of recognizing Oligo 7 files. -Version 7.34. Modified algorithm for PCR primers search. More primers are found after this search that pass the search criteria. -Version 7.35. Re-written most of the search procedures to make them compatible with the newest systems and fixed memory leaks. The File-open interface was changed for the Mac version, so it looks more OS-X native (non-Java like). -Version 7.36. Fixed bugs in Save dialog (Mac only) and improved the installer. Saving full analysis of Database saves also extinction coefficients. -Version 7.37. Fixed a minor bug in the Database that did not allow certain modifications of records. -Version 7.38. Added "Close Window" command in the File Menu. Fixed a bug in the nearest neighbor data calculations with dangling ends. -Version 7.39. Added special colors of amino acid type of Trp and Met in ORF Window. Changing the color coding in the ORF Window changes the amino acid symbols also in the Sequence Window. -Version 7.40. Fixed bug in Search Ranges Parameters that crashed the search for PCR primers when Non-overlapping product were chosen. -Version 7.41. Fixed bug in Search Batch searches that allowed oligos to be chosen with degenerate bases. -Version 7.50 Added 'Save Work' option. To activate it, please change the Startup option in the Preferences panel. -Version 7.51 Fixed bug in the Edit-Primer window that did not update the position number when a new primer was selected. -Version 7.52 Fixed bug in some dangling ends alignments free energy calculations, fixed the cursor shape in Mac version in Edit-Database window, and in Windows version Oligo automatically finds pdf help file. Also fixed a small bug that refreshed windows incorrectly. -Version 7.53 Fixed bug in calculation of PCR scores. It was related to certain dangling ends free energy calculations. -Version 7.54 Fixed bug in the Sequence window that calculated GC% contents of 1 nt. shorter oligo than displayed. Fixed a minor bug in the database edit window that sometimes did not update oligos correctly. -Version 7.55 (Mac only) Added authentication windows to make the registration possible on Lion (OS 10.7). -Version 7.56 Due to recent changes in Java the Internal Stability Window for the primers appeared blank when invoked te first time. Fixed. -Version 7.57 Fixed a bug that caused hanged search for siRNA in certain cases. -Version 7.58 Fixed a .wrk saving bug that ignored newly edited primers when the list of primers from the previous search was opened.