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 me
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 me
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
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
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
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
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 Dr. James A. Foster. 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
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
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
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