BacMet Tutorial


We encourage new BacMet users to use this online tutorial which is specially designed to explore the BacMet databases easily and more effectively. Most browsers (Firefox, Safari, Internet Explorer, Google Chrome) will work to get access to the BacMet webpages.

We have divided this section into

  1. BacMet database browsing
  2. Quick Search
  3. Advanced Search
  4. Performing BLAST Search
  5. Downloading Data
  6. Data Submission
  7. Screening Resistance Genes


  1. BacMet database browsing
  2. You can browse both databases ('BacMet Experimentally Confirmed database' and 'BacMet Predicted database') by selecting the database from the drop-down menu followed by the browsing options with compounds (metals, biocides or other compounds), biocide resistance genes, metal resistance genes and genes with both biocide and metal resistance potential. You can also browse the entire database. For example, if I am interested only in resistance genes associated with certain 'metal' of 'Predicted database' then I can mouse over the 'BROWSE' button in any page and then mouse ever the database I want to browse, followed by clicking on 'By Metals'.

    browsing

    Screenshot 1: BacMet database browsing


  3. Quick Search
  4. You may search and retrieve data using complete or partial keywords against all fields in both databases. Quick search can be performed in search page. You can search for resistance data with any keywords against both databases ('BacMet Experimentally Confirmed database' and 'BacMet Predicted database'). For example, if I am interested in resistance genes related to copper, I can enter the search term 'copper' in the provided search box. I will get an output table with all the resistance genes that match the search term 'copper' in any of the data fields.

    quick EXP search

    Screenshot 2: Quick search against BacMet Predicted database


    quick PREDICTED search

    Screenshot 3: Quick search against BacMet Predicted database

  5. Advanced Search
  6. Advanced search can be performed in the 'advanced search' web-page of BacMet. Multiple filters can be set in advanced search option. Advanced search will give an output in a html table format with the resistance genes information which matches the search criteria.

    1. You can select a particular 'compound' or a 'chemical class' from the dropdown menu.

    2. Gene Location can be chosen by clicking the checking boxes (Any, Chromosomal, or Plasmid).

    3. You can also filter the data by using certain keywords or text that a protein description contains (e.g. resistance)

    4. If you are interested in certain length of proteins, then that can be set by entering the protein length in the provided text box. Default protein sequence lengths have been set for the shortest protein as 50 aa and 2000 aa for longest protein respectively. The default values can be changed according to users' requirements.

    5. You can perform the advanced search against any of the two databases ('BacMet Experimentally Confirmed database' and the 'BacMet Predicted database') available in BacMet. Database can be selected by clicking the checking boxes.

    For example, if I am interested in resistance genes of 'Biguanides' chemical class from 'BacMet Predicted database' then I can select the 'class: Biguanides' from the drop-down menu of the compound/chemical-class list, followed by selecting the database as 'BacMet Predicted database'.

    advanced.search

    Screenshot 4: Selecting compound in advanced search option

    advanced.search

    Screenshot 5: Setting up filters in advanced search option

  7. Performing BLAST Search
  8. You have to select few options from the BLAST web-interface to perform a BLAST similarity search of their nucleotide or protein sequences against the BacMet databases. All the options in the BLAST web-interface are linked to BLAST documents to give a better idea before choosing the right options for BLAST run.

    1. You have to choose a BLAST programme (blastp or blastx).

    2. You have to select a database to search against ('BacMet Experimental database' or the 'BacMet Predicted database').

    3. You can copy and paste their sequence(s) in FASTA format in the provided text box or the FASTA sequence(s) can be uploaded from the local machine using the 'Browse' button in the BLAST web-interface.

    4. You can also select some other options such as setting up a subsequence of the input FASTA sequence to use for running BLAST search against the BacMet databases.

    5. Some advanced search options can be selected from the interface as well (see screenshot 5). Users can-
      - Set up an e-value (default value= 10)
      - Allow the low complexity (default: filtered) and mask (default: not filtered) filters
      - Select a matrix (PAM30, PAM70, BLOSUM80, BLOSUM62, or BLOSUM45)(default: BLOSUM62)
      - Allow ungapped alignment (default: not allowed)
      - Allow frameshift penalties in blastx (default: no penalties) and
      - Select some other advanced options

    6. Output options can be selected from te interface as well (see screenshot 6). users can-
      - Select the graphical overview (default: selected)
      - Select the alignment view (default: pair-wise)
      - Restricts the number of short descriptions of matching sequences in the output (default: 100)
      - Restricts the number of database sequences for which high-scoring segment pairs (HSPs) are reported (default: 50) and
      - Select a particular colour schema (default: no colour schema)

    BLAST

    Screenshot 5: Simple BLAST serach

    BLAST2.png

    Screenshot 6: Setting up 'BLAST search' advanced parameters

  9. Downloading Data
  10. All the data are available to download for large scale analysis from the 'Download' webpage. Files are available to download in a single set by downloading the compressed (.zip) file. Data Download can be performed by 'right clicking' on the file and 'clicking' the 'Save Link As' button to download file in the local machine. The downloaded compressed file can be uncompressed using the available functions in users' operating system (e.g. in Linux: unzip <zipped file name>)

    download.png

    Screenshot 7: Downloading files from BacMet

    Alternatively, you can download the individual file as you required in the same way as downloding the compressed file.

  11. Data Submission
  12. You can submit your data in the web-interface. The resistance gene data information need to be entered in the specified field of the provided submission form. All the submitted data will be manually checked and included in the BacMet database in the following updated version.

    data_submission.png

    Screenshot 8: Data submission to BacMet

  13. Screening Resistance Genes
  14. You can screen for biocide and metal resistance genes in genomes or metagenomes using our in-house developed software. Using the BacMet-Scan -h or BacMet-Scan -help commands you can read 'how to use the software' in the documentation.

    BacMet-Scan

    BacMet-Scan

    Screenshot 9: Screening resistance genes in genomes and metagenomes



BacMet database/website is designed and maintained by Chandan Pal

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