※Documentation:



USAGE:

In pTestis 1.0 database, we tried to make it 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 pTestis 1.0 provide the search option and advance options.

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

EXAMPLE: Please click on the "Example" button to search "Brca1" in Gene Name field. By clicking on the "Submit" button, the related proteins will be shown.

2. Advance Options. Three advance options are provided, including advance search, browse, BLAST search.

(1) Advance search allows you to input up to two terms to find the information more specifically. The querying fields can be empty if less terms are needed. The two 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 Breast cancer type 1 susceptibility protein homolog in mouse. The mouse Brca1 (PT-MM-00019) will be shown by clicking on the "Submit" button.

(2) Browse. You can browse the pTestis 1.0 database by species. With the default setting, you can directly click on the "Submit" button to browse all the acetylated proteins in the database.

(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 default is 0.01.

EXAMPLE: You can click on the "Example" button to load the protein sequence of human Histone H4. By clicking on the "Submit" button, you can find the related homologues in other species.




Frequently Asked Questions:

1. Q: How to use the local packages of the pTestis 1.0 database?

A: Please visit the latest version of pTestis 1.0 at http://ptestis.biocuckoo.org/db.php. Then please download and install the pTestis 1.0 database to your computer. Currently, the local packages of pTestis 1.0 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 was included in the installation package.

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

A: We have tested the online service and local packages of pTestis 1.0 database on several internet browsers, including Internet Explorer 6.0, Netscape Browser 8.1.3, Google chrome 4.1 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.

3. Q: I have a few questions which are not listed above, how can I contact the authors of pTestis 1.0?

A: Please contact the two major authors: Zexian Liu, Dr. Yu Xue, and Dr. Xuejiang Guo for details.