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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
The following tips will improve your user experience of PanDaTox:
- Sorting tables - organism, gene and intergenic region tables are sortable by clicking on the requested column header.
- Faster searching - multiple search keywords separated by commas are supported.
- Selecting multiple available search options - use the SHIFT and CTRL keys to select mutiple options available for searching.
- Faster blasting - the blast page supports input of up to 10 multi fasta sequences at once, given that the input size does not exceed 100 kb.
- Coverage plot viewer - all features of our covergae plot viewer are supported on Chrome and Firefox browsers.
It is therefore advised to use PanDaTox on either Chrome or Firefox.
- Tip box on every page - see tip box on each page for tips and info on available actions on page.
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:
- Summary - contains information on the whole genome, such as taxonomy, genome length, number of genes, number of unclonable genes,
number of decreased coverage genes, average plasmid and fosmid coverage depth, etc. (Example).
- Replicons - contains similar information as the Summary tab, but per each replicon in the genome (Example).
- Sequencing Libraries - contains informtaion on the different library sizes used for sequencing the genome (Example).
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:
- Gene Information - contains information on the gene, such as symbol, type, coordinates, product, COG, TIGRFAM ID, etc.
- Plasmid Coverage Information - contains the number of plasmids covering the gene, plasmid unclonability p-value,
and the prediction of gene plasmid clonability.
- Fosmid Coverage Information - contains the number of fosmids covering the gene, fosmid unclonability p-value,
and the prediction of gene fosmid clonability.
- Sequence - contains the gene nucleotide sequence, and protein sequence (if it is a coding gene).
In addition, the following buttons are available:
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Coverage Plot - links to a viewer displaying a plot of the coverage data, i.e. the number of clones covering each nucleotide in the gene's area.
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PanDaTox Homolog Hits - links to a page containing a table of all the homologous genes, along with their clonability data.
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Experimental Validation - link to experimental results of gene toxicity to E. Coli (This button will appear only if gene was validated).
Intergenic region information can be viewed by clicking on the ID of an intergenic region.
The PanDaTox database may be searched either by genomes or by genes.
Search by Genomes
- Go to the search page by pressing the "Search" navigation button.
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Select the criteria to search by from the drop down list.
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Type in a keyword to search for according to the chosen criteria.
Note: multiple keywords are allowed, separated by commas.
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Press "Display Available Options" button to see all entries matching keyword.
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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.
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Press the "Search" button to display the matching genomes.
Search by Genes
- Go to the search page by pressing the "Search" navigation button.
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Press on the "Genes" tab to go to Genes search
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Select the criteria to search by from the drop down list.
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Type in a keyword to search for according to the chosen criteria.
Note: multiple keywords are allowed, separated by commas.
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Press "Display Available Options" button to see all entries matching keyword.
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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.
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Use the "Filter by" section to narrow down search results.
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Press the "Search" button to display the matching genes.
Tips for better searching
- Multiple search keywords are allowed, separated by commas
- Search categories marked as "inexact" look for any matching entry which contains the entered keyword/s, other categories search require an exact match.
- When the available options matching the search keyword/s appear, multiple entries may be selected using the SHIFT or CTRL keys.
- All searches are case insensitive.
- Search keywords should be at least 3 characters long.
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:
- All gene nucleotide sequences.
- All coding gene protein sequences.
- All replicon nucleotide sequences.
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.
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Go to the blast page by pressing the "Blast" navigation button
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Uploade a file containing either nucleotide or protein sequences (in multi-fasta format) OR
paste the sequences in the text area.
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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.
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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.
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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.
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Press the "Blast" button.
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The blast hits will be displayed, with a collapsing secion for each query.
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Toggle between the +/- to display/hide the hits per query.
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Press the "Display raw blast report" button to view the actual blast program output and the sequence alignments.
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:
A full alignment spanning 100% of the query gene and 100% of the homologous gene (the black line is fully covered):
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.
- The X axis represents the genomic sequence of the replicon, with indication of bp coordinates.
Gene annotations are available along the X axis, with arrowheads represnting the strand on which the gene is located
(right and left arrowheads represent plus and minus strands, respectively).
- The Y axis represents the number of clones covering each nucleotide in the sequence.
- The green and red lines represent plasmid and fosmid coverage , respectively.
When hovering with the mouse over the lines, the exact coverage at that point will be displayed.
- A green or red rectangle below the X axis respresnts a plasmid or fosmid sequence gap , respectively (i.e. nucleotides with zero coverage)
- A grey shadow spanning a genomic sequence highlights the aread of interest which was jumped to by pressing the coverage plot icon.
(This area could be a gene, an intergenic region, etc.)
- The horizontal scroll bar should be used to see the coverage along the replicon sequence.
- The gene annotations are clickable and link to the corresponding gene page on PanDaTox.
- The viewer navigation toolbar enables the user to :
- Jump to a specific position along the displayed replicon by entering coordinates and pressing "Go".
- Scan the replicon by jumping 125,000 bp downstream or upstream by pressing the "Next" or "Back" buttons, respectively.
- Display or hide the legend by checking or unchecking the "Legend" check box , respectively.
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