Help

Basic usability tips
Viewing organism information
Viewing gene information
Viewing intergenic region information
Searching PanDaTox
Blasting your own sequence against the PanDaTox collection
Grpahical display of homologous sequences
Coverage plot viewer


Basic Usability Tips

The following tips will improve your user experience of PanDaTox:


Viewing Organism Information

Organism information can be viewed by clicking on an organism name, from any page on the PanDaTox website.
The genome information page organizes the data in three clickable tabs:


Viewing Gene Information

Gene information can be viewed by clicking on a gene's locus tag, from any page on the PanDaTox website (Example).
The gene informtaion page contains four informational tables:

In addition, the following buttons are available:


Viewing Intergenic Region Information

Intergenic region information can be viewed by clicking on the ID of an intergenic region.


Searching PanDaTox

The PanDaTox database may be searched either by genomes or by genes.

Search by Genomes

  1. Go to the search page by pressing the "Search" navigation button.
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  2. Select the criteria to search by from the drop down list.

  3. Type in a keyword to search for according to the chosen criteria.
    Note: multiple keywords are allowed, separated by commas.

  4. Press "Display Available Options" button to see all entries matching keyword.

  5. Select the entries you would like to search for or check the "All" checkbox to select all entries.
    Note: multiple entries may be selected using the SHIFT or CTRL keys.

  6. Press the "Search" button to display the matching genomes.

     

 Search by Genes

  1. Go to the search page by pressing the "Search" navigation button.
  2. Press on the "Genes" tab to go to Genes search
     

  3. Select the criteria to search by from the drop down list.

  4. Type in a keyword to search for according to the chosen criteria.
    Note: multiple keywords are allowed, separated by commas.

  5. Press "Display Available Options" button to see all entries matching keyword.

  6. Select the entries you would like to search for or check the "All" checkbox to select all entries.
    Note: multiple entries may be selected using the SHIFT or CTRL keys.

  7. Use the "Filter by" section to narrow down search results.

  8. Press the "Search" button to display the matching genes.

 Tips for better searching


Blasting your own sequence against the PanDaTox collection

The "Blast" page provides a search engine for user sequences. Users can upload nucleotide or amino acid sequences
in multi-fasta format and blast against the following PanDaTox collections:

Blast hits are presented for each query. The results refer to the genes/replicons in the PanDaTox database,
and link to PanDaTox info for each of the results.
In addition, the raw blast output and alignment are available for browsing.

  1. Go to the blast page by pressing the "Blast" navigation button

  2. Uploade a file containing either nucleotide or protein sequences (in multi-fasta format) OR
    paste the sequences in the text area.

  3. Select the blast program to use:

    • blastn - compares a nucleotide query sequence against a nucleotide sequence database
    • blastp - compares an amino acid query sequence against a protein sequence database
    • blastx - compares a nucleotide query sequence translated in all reading frames against a protein sequence database
       
    Note: the selected program must match the type of input sequence:

    • If the input sequence contains nucleotide sequences, the valid programs are: blastn , blastx.
    • If the input sequence contains protein sequences, the valid program is blastp. 
  4. Select the PanDaTox collection to blast the sequences against:

    • PanDaTox gene collection (bp sequences) - nucleotides sequences of all the genes in the PanDaTox database.
    • PanDaTox replicon collection (bp sequences) - nucleotides sequences of all the replicons in the PanDaTox database.
    • PanDaTox protein collection (aa sequences) - protein sequences of all the coding genes in the PanDaTox database.
       
    Note: the selected collection must match the selected program:

    • PanDaTox gene collection can be used with the following programs: blastn.
    • PanDaTox replicon collection can be used with the following programs: blastn.
    • PanDaTox protein collection can be used with the following programs: blastp , blastx.
  5. If required, modify the deafult E-value cut off. The hits displayed will be the ones with an E-value lower than the one indicated here.
    Note: An E-value < 10-3 of an alignment means that that alignment is highly unique, and not due to error.
    Lower E-value thresholds are more stringent, and report fewer matches.

  6. Press the "Blast" button.


  7. The blast hits will be displayed, with a collapsing secion for each query.

  8. Toggle between the +/- to display/hide the hits per query.

  9. Press the "Display raw blast report" button to view the actual blast program output and the sequence alignments.

 


Grpahical display of homologous sequences

In tables presenting homologous genes or blat hits, a graphical display of alignment is also available.
A thin black line represents the query / hit sequence, and the red bar placed on top of it
represents the part of the sequence that was aligned.

Examples:

A partial alignment between 20% of the downstream sequence of a query gene and 30% of the downstraem sequence of the homologous gene:

partial alignment image example

A full alignment spanning 100% of the query gene and 100% of the homologous gene (the black line is fully covered):

full alignment image example


Coverage plot viewer

The coverage plot viewer provides a graphical means for examining nucleotide coverage of a certain genomic sequence.

Note: Firefox and Chrome browsers fully support viewer's functionality, while Internet explorer does not.
It is advised to use Chrome or Firefox browsers when viewing coverage plots.

full alignment image example