Signature OligoDatabase

OligoDBViewer download (12.8 Mb)

last debugging: 2011.04.05

Database download:

bacteria

892 genomes

142 Mb

last update by 2011.04.05

Here we want to present a database of 172,636 selected 8 to 14mer oligonucleotides, which frequencies varies significantly in different bacterial genomes. The database is supplied with a GUI to allows database browsing and selection of the best discriminative words for a given set of genomes or taxonomic units. A database file is available for download containing the information about frequencies of signature words in 724 bacterial genomes. Users may add new genomes to the database or remove them from the database to keep it updated and focused on the species of interest. The program was developed for comparative genomics and binning unknown sequences or groups of sequences to bacterial taxonomic units.

Download the file OligoDBViewer.zip from the site http://www.bi.up.ac.za/SeqWord/downloads/. Unzip file to a selected directory. A folder OligoDBViewer will appear with several files and subordinate folders inside. Run Python OligoDBViewer.exe.py. A starting window of the program will appear.

Use the command File->Open to open a database file. The viewer cannot create a new empty database. An example of a small database example.wdb (35.1 Mb, 174 bacterial genomes) you may find in the subfolder db. Select this file and click Open. You may download the database file bacteria.wdb. At the time of writing this document, the database size was 118 Mb and it contained 733 bacterial genomes. However, this database is regularly updated and the real size of the database file may be bigger.

1. List of taxonomic units
The list of taxonomic units is three levels deep: classes, genera and genomes (the latter corresponds to a chromosome with a specific NC accession number).
Multiple items in the list may be selected simultaneously by mouth clicking. To open a taxonomic unit, double-click on it. Double-click again to collapse the list of subunits.
2. Toolbar
    ▪  Open – open another database file, the same as File->Open;
    ▪  Save – save changes in the database, same as File->Save or File->Save as;
    ▪  Find – open a dialog Search genome that allows finding a genome by its taxonomy or NC accession number. You may choose Edit->Search.
    ▪  Edit – open a dialog to edit the active (last clicked) taxon as shown below. Alternatively choose Edit->Edit.

    ▪  New taxon – first asks for the file in FASTA or GenBank format with the genome sequence (alternatively choose Edit->Add). Program automatically calculates frequencies of the signature words in a given genome. Next a dialog pops up (shown right) where class, genus, species, strain and accession must be filled in. If a GenBank (.gbk) file was provided, program tries to identify the phylogeny of the organism basing on the stored data. The process of word frequency calculation is time and computer memory consuming. It'd better to run it on a remote server using a command line utility dbupdate_cmd.py.
    ▪  Delete – remove the selected taxon from the database, same as Edit->Delete.
Next three buttons Select all, Reverse selection and Deselect all operate selecting of items in the list.

Users may create own databases by saving the existing database under a new name followed by adding and removing genomes in the databases. Two existing database then may be merged by the command File->Merge database.

1. Selection of diverse words.
First select in the list the taxonomic units you want to compare. The program will analyze frequencies of words in all genomes belonging to these units. User may select units of different levels, for example: one class and several genera of another class. Having all taxonomic units selected, click the button Select diverse words or choose Command->Select diverse words. A filter setting dialog will pop up (will be discussed later, at this stage it is not recommended to use the filter as it will significantly slow down the program). Click OK and a list of selected words (100 by default) with the highest discriminative power will be shown on the right report panel.

Description of the command buttons on the report panel is given below.

2. Selection of common abundant words.
In this mode the program selects the words which are abundant in all selected taxa. Repeat the same steps as in the previous task but click the button Select common abundant words or choose Command->Select abundant words.

3. Selection of common rare words.
In this mode the program selects the words which are rare in all selected taxa. Repeat the same steps as in the first task but click the button Select common rare words or choose Command->Select rare words. The resulted list of words will be shown on the right panel.

4. Comparison of different taxonomic units.
The program selects words with the minimal divergence within the taxonomic units but the maximal intrataxonimic divergence. Choose Command->Compare taxa. A dialog will pop up shown below:

Select a radio-button to display the list of classes, genera or species. Then in the scrolled listbox chouse the taxonomic units to compare. User may click Show/Hide Filter button to set the word filter (will be discussed below), but at this stage it is not recommended to use the filter as it will significantly slow down the program.
Click OK. The resulted list of top scored words will be shown on the right panel.

5. Confronted comparison of taxonomic units.
In this mode the program selects the words, which will be the most useful to distinguish a selected taxon from a set of counterpart taxonomic units; or the words which are abundant in the selected taxon but rare in the counterpart taxa; or contrary, the words which are rare in the selected taxon but abundant in the counterpart taxa.
Choose Command->Confronted comparison. A dialog will pop up shown below:

Select the radio-button to display the list of classes, genera, species or chromosomes. Choose the radio-button +/-, +++ or -- to select the divergent, abundant or rare word selection, correspondingly. Then in the scrolled listbox select the sample taxonomic unit and click the button Select. The name of the taxon will appear in the area Selected taxon, the button Select turns to Reset and the listbox will allow multiple selection of taxonomic units. Now select the taxonomic units against which you want to compare the sample taxon and click the button Add to display these items in the list To compare with. User may click Show/Hide Filter button to set the word filter (will be discussed below), but at this stage it is not recommended to use the filter as it will significantly slow down the program.
Click OK. The resulted list of words will be shown on the right panel.

Filter settings may be done prior to running the word selection algorithms described above, but we recommend not to set filtering of word permutations, wordshifts and constituent words at this stage, as it may make the program too slow.
More practical will be filtering of the words in the resulted list. Not only it is faster, but word filtering in this case is reversible.
To open Word filter dialog, click on the button Set Filter. Following options are available in the dialog:
    ▪  Filter permutations – click on the check button to activate the filter and select the value in the combo box. The program will remove from the list all words with lower scores, which may be obtained from the outscored word by one or several nucleotide replacements;
    ▪  Filter wordshifts – click on the check button to activate the filter and select the value in the combo box. The program will remove from the list all words with lower scores, which may be obtained by shifting the outscored word to one or two nucleotides leftward or rightward;
    ▪  Filter constituents – click on the check button to activate the filter and select the value in the combo box. The program will remove from the list all words that are constituent elements of longer words already present in the list;
    ▪  Word length thresholds – set the minimal and the maximal length of the words in the range from 8 to 14 nucleotides;
    ▪  Score – in all algorithms the words are scored in the range from 0 to 10. Set the minimal value of the score for the words to be selected;
    ▪  Top – maximal length of the list of selected words.
    ▪  Redun – maximal number of redundant words.

	G1	G2	G3	G4	G5	G6
W1	+++	+++	+++	--	--	--
W2	+++	+++	+++	--	--	--
W3	+++	+++	++	--	--	--
W4	++	--	+++	--	++	--

Enter an oligonucleotide of 8 to 14 bp long into the field Search for and click on the button >> to add this oligonucleotide to the list Selected words. Alternatively, you may enter only a few starting letters (nucleotides) of the word and click the button Search. A list of all words in the database starting with the entered letters will appear in the listbox Available words. Click on the word of interest and then click on the button >> to add this oligonucleotide to the list Selected words.
Words may be uploaded to the list Selected words from a text file using the button Upload. The list may be created manually or exported from the Report panel using the button Export. 
Next select taxonomic units in the listbox Selected genomes and click on the button OK. The program will calculate either the discrimination scores for selected words and taxonomic units, if the radio button Taxa is set; or displays frequencies of the selected words as shown below, if the radio button Words is set:

To open the current help file in the browser on your computer, choose the command Help->Help.

python oligodb_cmd.py -i input.txt -d bacteria -o output.out -w words.txt -p 0 -f 0,0,0,8,14,0,10000,10,10

    ▪  -i – the name of the input file with the list of NC accessions for which the discriminative signature words are to be found (input by default). The input file has to be specifically formatted. The file may be obtained by selecting the genomes or taxonomic units of interest in GUI main window and exporting their accession numbers to a text file using the command File->Export accessions. Alternatively, use the command line program infile_cmd.py that is described below.
    ▪  -d – the name of the database (bacteria by default). It is supposed that the database file with the same name and the extension .wdb is in the subfolder db of the current folder.
    ▪  -o – the name of the output report file (output by default). The file format will be exactly the same as when the button Export on the Report panel is used (see above). Later this file may be displayed on the Report panel using the command File->Import report.
    ▪  -w – optional name of a text file with the list of pre-selected words. By default this option is not set. It is similar to uploading the word list file in the dialog Search words and running the program for the taxa selected in the same dialog with the radio button Taxa set on (see above).
    ▪  -p – program number (by default 0):
            0 – select diverse words or compare taxa if accessions are grouped by taxa in the input file;
            1 – select abundant words for genomes or taxa;
            2 – select rare words for genomes or taxa;
            3 – do confronted comparison. First genome or first taxa in the list are selected as an outgroup.
    ▪  -f – the string of filter settings in the order "m,sh,c,wl1,wl2,sc,top,red,sim" where:
            m – number of permutations to filter (may be set as an absolute number or as a percentage);
            sh – left/right shift length to filter (may be set as an absolute number or as a percentage);
            c – length of constituent words to filter;
            wl1 – minimal word length (in a range from 8 to 14 but smaller than wl2 );
            wl2 – maximal word length (in a range from 8 to 14 but bigger than wl1);
            sc – score threshold;
            top – number of top scored words to select (by default 10000);
            red – maximal number of redundant words in the list (by default 10);
            sim – similarity threshold to consider words as redundant (by default 10%, see above);
 

This program is used to prepare an input file for the program oligpdb_cmd.py that was described above.

python infile_cmd.py -t 2 -d bacteria -o output.out -n NC_009725,NC_003997,...

    ▪  -n – comma separated list of accessions or taxonomic units;
    ▪  -t – taxonomic level (2 by default):
            0 – bacterial classes: -n  Firmicutes,Fusobacteria,... ;
            1 – genera: -n  Firmicutes|Bacillus,Firmicutes|Clostridium,...;
            2 – accessions: -n NC_009725,NC_003997,...;
            3 – species: -n Firmicutes|Bacillus|subtilis,Firmicutes|Bacillus|cereus,....
    ▪  -o – output file that may be used as an input file for the program oligpdb_cmd.py.

Selection of high scored words and filtering of the word list may be separated to achieve better performance. Use the program filter_cmd.py to filter the output file of the program oligpdb_cmd.py with the word list report.

python filter_cmd.py -i report.txt -o filtered_report.txt -f 30%,1,1,8,14,0,100,10,10%

    ▪  -i – name of the input report file that is to be filtered;
    ▪  -o – name of the output file;
    ▪  -f – the string of filter settings in the order "m,sh,c,wl1,wl2,sc,top,red,sim" where:
            m – number of permutations to filter (may be set as an absolute number or as a percentage, by default 30%);
            sh – left/right shift length to filter (may be set as an absolute number or as a percentage, by default 1);
            c – length of constituent words to filter (by default 1);
            wl1 – minimal word length (in a range from 8 to 14 but smaller than wl2 );
            wl2 – maximal word length (in a range from 8 to 14 but bigger than wl1);
            sc – score threshold;
            top – number of top scored words to select (by default 100);
            red – maximal number of redundant words in the list (by default 10);
            sim – similarity threshold to consider words as redundant (by default 10%, see above);

The database may be updated with new genomes represented by FASTA or GenBank files.

python dbupdate_cmd.py -i input -d bacteria

    ▪  -i – name of the input folder - input by default;
    ▪  -d – the name of the database (bacteria by default). It is supposed that the database file with the same name and the extension .wdb is in the subfolder db of the current folder.
Before running this program, copy source genbank files to the input directory. In contrast to the function Edit->Add that may parse both FASTA and GenBank file formats, this command line program can read only GenBank files.