In MiCroKit 3.0 database, we tried to make it more powerful and convenient to be used. The online service and local packages were provided. This USAGE is prepared for the online service. For usage of local packages, please download the Manual. The MiCroKit 3.0 provide the search option and advance options.

1. Search. You can input one or multiple keywords (separated by space character) to search the MiCroKit database. The search fields including MiCroKit ID, Localization (Centrosome, kinetochore or midbody), UniProt Accession, Protein Name, Protein Alias, Gene Name, Gene Alias, and Function.

EXAMPLE: Please click on the "Example" button to search "CENP-E" in Protein Alias field. By clicking on the "Submit" button, the related microkit proteins will be shown.

2. Advance Options. Five advance options are provided, including advance search, browse, BLAST search, orthologous group browse, and pairwise orthologous browse.

(1) Advance search allows you to input up to three terms to find the information more specifically. The querying fields can be empty if less terms are needed. The three terms could be connected by the following operators:

exclude: If selected, the term following this operator must be not contained in the specified field(s)
and: the term following this operator has to be included in the specified field(s)
or: either the preceding or the following term to this operator should occur in the specified field(s)

EXAMPLE: You can click on the "Example" button to load an instance, which could search kinetochore protein aurora in yeast. The budding yeast IPL1 (MCK-SC-00096) will be shown by clicking on the "Submit" button.

(2) Browse. You can browse the MiCroKit 3.0 database by species and/or localizations (Centrosome, kinetochore or midbody). With the default setting, you can directly click on the "Submit" button to browse midbody proteins in C. elegans.

(3) BLAST search could be used to find the specific protein and/or related homologues by sequence alignment. This search-option will help you to find the querying protein accurately and fast. Only one protein sequence in FASTA format is allowed per time. The E-value threshold could be user-defined, while the species information could be specified. The default parameters of E-value and species are 0.01 and H. Sapiens, respectively.

EXAMPLE: You can click on the "Example" button to load the protein sequence of human Baculoviral IAP repeat-containing protein 5. By clicking on the "Submit" button, you can find the related homologues in H. Sapiens.

(4) Orthologous group browse. In MiCroKit 3.0 database, the pairwise orthologous information was computed with the InParanoid program (Remm M et al., 2001; Kevin P et al., 2005), while the orthologous group information was further defined based on similar approaches in COGs (Clusters of Orthologous Groups of proteins) (Tatusov RL et al., 1997). Three operators are provided:

Default: Either included or excluded. If all species were set in "Default", all orthologous groups in MiCroKit 3.0 will be shown.
Include: Select a species. For any orthologous group, there must be an ortholog protein in this species.
Exclude: Exclude a species. For any orthologous group, there must be no ortholog proteins in this species.

EXAMPLE 1: You can click on the "Example1" button to browse the microkit proteins conserved in all species. Totally, there are 206 orthologous groups shown, including 482 microkit proteins and 1192 UniProt proteins (Not included in MiCroKit due to lack of experimental evidence).

EXAMPLE 2: You can click on the "Example2" button to show the microkit proteins that are conserved in human and fruit fly but not in budding yeast.

(5) Pairwise orthologous browse. The pairwise orthologous information could also be viewed in details. The Score (bits), E-value, Identities and Positives from BLAST results are provided. For an orthologous group containing more than one protein in a species, only the orthologous pair with the highest E-value > Identities > Positives was calculated and represented as the similarity for this group.

EXAMPLE: You can directly click on the "Submit" button to browse the orthologous information between mouse and human, while the identity is equal or greater than 20%. For the first hit of "MCK-MM-00063 MCK-HS-00358", the Score (bits), E-value, Identities and Positives are calculated directly. For the second hit of "P97477 MCK-MM-00076 MCK-MM-00056 MCK-HS-00200 MCK-HS-00278 MCK-HS-00359", the similarity results for the group were calculated between "P97477" and "MCK-HS-00200" (with the highest E-value score). You can directly click on the MM, HS, Score, E-Value, Identities, or Positives to resort the results.

Frequently Asked Questions:

1. Q: What is the rationale of "seeing is believing"? And why is it any good?

A: The rationale of "seeing is believing" is important for studying the plasticity and dynamics of Midbody, Centrosome and/or kinetochore. There are a lot of proteins could interact with microkit proteins, but be not localized on these areas. It's almost the only way to unambiguously verify a microkit protein under fluorescent microscope. other approaches can only generate hypothetical information..

2. Q: What's the difference between 1.0 & 2.0 and the MiCroKit 3.0 database?

A: First, newly discovered MiCroKit proteins were collected into 3.0 database. All features, annotations and advance options in 1.0 or 2.0 were totally reserved in MiCroKit 3.0 database. Additionally, we added two advance options in MiCroKit 3.0 database, including orthologous group browse, and pairwise orthologous browse. The pairwise orthologous information was computed with the InParanoid program (Remm M et al., 2001; Kevin P et al., 2005). The orthologous group information was further defined based on similar approaches in COGs (Clusters of Orthologous Groups of proteins) (Tatusov RL et al., 1997). The orthologous information for each microkit protein was provided in MiCroKit 3.0 database.

3. Q: How to use the local packages of the MiCroKit 3.0 database?

A: Please visit the latest version of MiCroKit 3.0 at http://microkit.biocuckoo.org/search.php. Then please download and install the MiCroKit 3.0 database to your computer. Currently, the local packages of MiCroKit 3.0 database were implemented in JAVA 1.5 (J2SE 5.0) and could be installed on a computer with Windows/Linux/Unix/Mac OS. And we also wrote a manual for users which included in the installation package..

4. Q: I can't open the program properly, what should I do?

A: We have tested the online service and local packages of MiCroKit 3.0 database on several internet browsers, including Internet Explorer 6.0, Netscape Browser 8.1.3 and Firefox 2 under Windows XP Operating System (OS), Mozilla Firefox 1.5 of Fedora Core 6 OS (Linux), and Safari 3.0 of Apple Mac OS X 10.4 (Tiger) and 10.5 (Leopard). The online service could be directly visited or browsed, while the local packages could be directly installed on your computer. Additionally, if you can not view the program properly, please send use an email and tell me the OS information on your computer. We will resolve the problem ASAP.

5. Q: I have a few questions which are not listed above, how can I contact the authors of MiCroKit 3.0?

A: Please contact the two major authors: Dr. Yu Xue, and Dr. Jian Ren for details.

MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore.
Jian Ren, Zexian Liu, Xinjiao Gao, Changjiang Jin, Mingliang Ye, Hanfa Zou, Longping Wen, Zhaolei Zhang, Yu Xue and Xuebiao Yao. Nucleic Acids Research. 2010;38:D155-D160
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