Historic Changes to the Software

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MiCA includes 28 forward and 31 reverse primers, and 71 restriction enzymes.
P&G
IIDS
BCB Program
Biological Sciences
University of Idaho

March 29, 2011: The long overdued database updates have been completed. All RDP databases have been updated to Relesae 10, Update 26. The RDP archaeal databases contain 10,475 good quality and 70,108 16S sequences. The bacterial databsaes contain 703,222 good quality and 1,542,955 16S sequences. The updates also included databses (LSU Parc, LSU Ref, SSU Parc and SSU Ref) from the SILVA rRNA database project. Finally, the new greengenes database contains 407,309 16S rDNA sequences. If you encounter any problem, please let RCDS know.
October 11, 2010: Several databases on MiCA have been updated recently. All RDP databases have been updated to Release 10, Update 22. The RDP archaeal databases now contain 9,728 good quality and 62,211 16S sequences. The bacterial databases contain 606,188 good quality and 1,356,286 16S sequences. The updates also included databases from the SILVA rRNA database project. The SSU Parc (16S/18S) database contains 1,471,257 sequences and SSU Ref 512,037. These databases include sequences for all three domains of life (Bacteria, Archaea and Eukarya). Finally, the greengenes database has been updated with 510,111 16S rDNA sequences. If you encounter any problem, please let RCDS know.
December 28, 2009: The search algorithms on MiCA have been implemented to run concurrently using multithreading. Multithreading allows each search to run on multiple processors simultaneously. The speedup is quite dramatic. As an example, an in silico digestion will now only take 13 seconds to complete, instead of a minute. I didn't get a chance to run extensive tests on the new implementations. If you notice any inconsistencies or problems, please let RCDS know.
June 13, 2009: The RDP databases have been updated to release 10, update 12. This update was released on June 10, 2009. The new databases contain 322,864 good quality and 776,206 16S bacterial rRNA sequences. The archaeal databases contain 7,882 good quality and 44,988 16S rRNA sequences. All gaps are removed. It is important to note that each in silico digestions will take a much longer time to complete as the number of sequences increases. Please wait for a few additional minutes before clicking the result link.
March 24, 2009: If you use the data generated by MiCA in a publication, please cite: Shyu, C., Soule, T., Bent, S.J., Foster, J.A., Forney, L.J. (2007) MiCA: A Web-Based Tool for the Analysis of Microbial Communities Based on Terminal-Restriction Fragment Length Polymorphisms of 16S and 18S rRNA Genes. Journal of Microbial Ecology 53:562-570.
May 7, 2008: The RDP database has been updated to release 9.60. This update was released on April 22, 2008. The new database contains 511,847 unaligned 16S rRNA gene sequences. All gaps are removed.
May 6, 2008: It has been a while since the last updates on the database. The 16S rRNA sequences for the analysis of gut organisms (human, mouse, pig, and ruminant) has been updated. This database was provided by Sanjiv Bhandari. It is deisgnated as H.Q. 16S Gut Organisms on MiCA.
August 30, 2007: The FAQ (frequently asked questions) has been updated. The FAQ section contains several most frequently asked questions and corresponding answers about MiCA. Please visit the FAQ section first. Your questions may already have been answered.
July 12, 2007: A new feature has been added to MiCA. If you only use one fluorescently labeled primer (forward primer is assumed), please use PAT+ for analysis. PAT+ only requires the profile generated using the forward primer. For in silico amplification to perform properly, the reverse primer, however, is still required.
June 29, 2007: The database has been updated to RDP9.1, update 51. The database contains 380,520 16S rRNA sequences. In addition, the default database has been set to the one that only contains sequences with good quality (> 1,200bps). Please be aware that the time required to complete a query increases significantly, as the number of sequences increases rapidly.
July 26, 2006: A new database has been added to MiCA. The database contains 95,140 16S rRNA gene sequence download from http://greengenes.lbl.gov. The greengenes database project was created by T. Z. DeSantis, I. Dubosarskiy, S. R. Murray, and G. L. Andersen.
July 24, 2006: I (Conrad Shyu) am no longer the system administrator of MiCA. Please send all questions and comments to RCDS. If you have any technical questions about MiCA, you can still email me. I will try to answer them as soon as possible.
July 14, 2006: I have completed a major updated on the APLAUS+ web interface and algorithm. The new algorithm can better estimate the relative abundance based on the submitted data. The output is also much easier to understand. The new algorithm requires separate files for the forward and reverse fragments. Please check out the help file for more information.
May 10, 2006: The database has been updated to RDP9, update 38. Currently, there are 210,005 16S rRNA sequences in the database. Several other customized databses have also been added to MiCA.

September 9, 2005: Some minor changes have been made to the web interface in order to support ever increasing numbers of databases on MiCA. Two additional databases have been added; (1) full length of high quality 16S sequences from the colon of humans, pigs, and the rumen, (2) representative sequences of the major lineages of bacteria in the colon of mammals.

October 29, 2004: The MiCA database has been updated to Ribosomal Database Project-II Release 9. The new database contains 108,781 unaligned and annotated Bacterial small-subunit rRNA sequences.
March 7, 2004: The MiCA query program has been updated. Ambiguities are permitted in the restriction enzymes. Primer specificity and enzyme fidelity analysis pages are now fully functional. The community profile analysis pages are still under construction. We are currently updating the online help pages.
September 4, 2006: MiCA is currently running on the new server. Everything should be fully functional. If you experience any problems, please contact the system administrator. The old server will be shut down shortly.
September 4, 2003: We have updated the database to the newest version of RDP. The new database contains 62,762 bacterial and 1,172 archaeal sequences. Therefore, queries will take much longer to run. In addition, we are migrating to entire web site to a new and powerful server. The new server will have a new domainname, http://mica.ibest.uidaho.edu/, and the old one will phase out shortly.
February 9, 2003: The MiCA database has been restored. We are still working on migrating the updated RDP data into the MiCA database. If you experience any problems, please notify us.
July 31, 2002: Multiple digest with at most three enzymes are now possible. Query can return all fragment lengths or only the shortest ones. The output is available in CSV (Comma Separated Values) and plain-text format. CSV file format allows data to be easily retrieved into spreadsheet or database programs. The majority of spreadsheet applications, such as Linux Gnumeric or Microsoft Excel, can read and write CSV files. Internet Explorer will invoke Excel within the browser. For Netscape users, please save the file first and load it with any spreadsheet program.

If you use the data generated by MiCA in a publication, please cite:

Shyu, C., Soule, T., Bent, S.J., Foster, J.A., Forney, L.J. (2007) MiCA: A Web-Based Tool for the Analysis of Microbial Communities Based on Terminal-Restriction Fragment Length Polymorphisms of 16S and 18S rRNA Genes. Journal of Microbial Ecology 53:562-570.