BOMM Help

Written by kwu and cliu
Last updated: Thursday, April 18, 2014

Welcome to Barcode of Medicinal Material (BOMM) system. Detailed description of the system can be found in the manuscript describing the system. Briefly, BOMM contains a database and a species identification module. The database contains the DNA barcode sequences associated with each medicinal animal,plant and fungal species. Particular information related to the medicinal plant species are provided in a monograph like page. Below is a brief description on the usage of the BOMM system.


Table of Contents

    Installation of the Java and configuration of settings

    The Search Page

    The Species Information Page

    The HMM Logo Page

    Visualization of multiple sequence alignment using Jalview

    The Browse Page

    The Identify Page


Installation of the Java and configuration of settings

  In order to use the Jalview, you need to install the newest version of Java and change the security settings accordingly.

You can download Java in: http://java.com/

For Windows 7 user, please follow the instructions below to change the security settings:

  1. Click to enter the “Control Panel”.
  2. Click the “Programs” (Figure 1.1).
  3. 1.1
    Figure 1.1 Control Panel

  4. In the pop-up window, find and click the icon for Java (Figure 1.2).
  5. 1.2
    Figure 1.2 Program Window

  6. In the Java Control Panel, click the “Security” tab (Figure 1.3).
  7. 1.3
    Figure 1.3 Java Control Panel

  8. Two ways to change the Security of Java.
  • Add our Website http://www.dnabarcode.net/ to the "Exception Site List" (Figure 1.4 and Figure 1.5).
  • 1.4
    Figure 1.4 Java Control Panel Under the Security Tab

    1.4
    Figure 1.5 Exception Site List

  • Change the security level to “Medium” and click “ok” (Figure 1.6). But, we don't recommend to do that.
  • 1.4
    Figure 1.6 Java Control Panel Under the Security Tab.

 

The Search Page

  • Welcome to the the search page (Figure 2.1).
  • 2.1
    Figure 2.1 Search Page


  • In this page (Figure 2.1) you can search the medicinal material by the Latin name, English name,Ping Ying name and the Taxid. After submitting a query string you will see the result (Figure 2.2).

    2.2
    Figure 2.2 Search Result Page

  • Choose the medicinal material you would like to get more information, and you will be directed to a species information page (Figure 3.2).
  •  

    The Species Information Page

  • When using the search and browse modules of BOMM, you will see a species page as shown in Figure 3.2.
  • For the first time you enter BOMM website, you might see a popup window showing a message for Security Warning (Figure 3.1). Please click the “run” button.
  • You might be asked “Allow www.dnabarcode.net/" run “Java Platform SE 7 U”? ”, Please select “Allow…” or “Allow and Remember” to continue.

    3.1
    Figure 3.1 Security Warning

  • In the “Species Information Page”, you will see five tables (Figure 3.2). Note that “NA” stands for “not applicable” or “not available”.

    1. Table A shows the medicinal material’s taxonomy information.
    2. Table B shows the pharmacological properties of the medicinal materials. For “Ingredients”, each number is a hyperlinked (marked with a in Figure 3.2) to additional information about the ingredients.
    3. Table C shows whether or not the medicinal materials belong to any particular list.
    4. Table D shows detailed information of the DNA barcode sequences for the medicinal materials. The meaning of each fields are explained below:
      1. “Length”: the maximum length of the alignment.
      2. “Num of Sequence”: the total number of sequences in the sequence alignment.
      3. “Num of Residues”: the number of residues in total in the alignment.
      4. “Is Flush”: whether or not the alignment is flush, that is, all of sequences having the same length.
      5. “Percentage Identity”: the average of pairwise percentage identity of sequences in the alignment.
      6. “Get HMM Logo” (marked with b in Figure 3.2): links to "HMM logo page” (Figure 4.1).
      7. “Show Alignment”: just click the “Start Jalview” button (marked with c in Figure 3.2) to activate Jalview, through which the alignment can be reviewed in detail (Figure 5.1).
    5. Table E lists external links to the medical materials you are examining, e.g. photo, reference, and collection information.

    3.2
    Figure 3.2 Species Information Page

     

    The HMM Logo Page

  • When clicking the “Get HMM Logo” button (marked with b in Figure 3.2) in the “Species Information Page” , you will be directed to the “HMM Logo page” (Figure 4.1).
  • The Y axis (marked with a in Figure 4.1) shows the information Content in bits. The X axis ( marked with b in Figure 4.1) shows the nucleotide position in the HMM models. The panels (marked with c in Figure 4.1)presents “occupancy”, “insert probability” and “insert length” respectively. For detailed information, please go to http://skylign.org/ . You can also download the HMM file following the link at the bottom of the LOGO.

    4.1
    Figure 4.1 HMM Logo Page

     

    Visualization of multiple sequence alignment using Jalview

    When clicking the “Show Alignment” button ( marked with c in Figure 3.2) in “Species Information Page” , a Jalview panel will popup (Figure 5.1). Jaview is a powerful software tool for the visualization of sequence alignments. For detailed information,please go to http://www.jalview.org/about/Documentation .

    5.1
    Figure 5.1 Jalview Interface

     

    The Browse Page

    BOMM provides two different methods to retrieve the information for a particular medicinal species through “Browse” (Figure 6.1) and “Search” modules respectively (Figure 3.2). The “Browse” page currently only supports the “Latin name” ,"English name"and “Chinese name” as the query term. Additional query term will be added later on.

    6.1
    Figure 6.1 Browse Page

     

    The Identify Page

    BOMM provides two methods to identify the species of a given query sequence, one is based on finding the nearest neighbor individual sequences and the other is based on finding the nearest neighbor HMM.

  • the Sequence-based method
  • From the query page (Figure 7.1), user can submit the sequence in fasta file, and then click “Submit” button. The intermediate results and a conclusion will be provided.

    7.1
    Figure 7.1 Identify by Distance

  • the HMM-based method.
  • From the query page (Figure 7.2), user can submit a query sequence in fasta file, select the HMM database to search against. The database can be a combined database that contains all HMMs for all DNA barcode markers, as well as HMMs for particular DNA barcode marker. Click “Submit” ,then the results will be generated including links to detailed inforamtion for species as well as recommended species identity.

    7.2
    Figure 7.2 Identify by HMM

     

    For any questions or comments, please feel free to send email to ipaginfo@gmail.com .

    We are dedicated to make BOMM a central resource for molecular authentication of medicinal materials.