Help for DB-AT (DataBase of Apicomplexa Transcriptomes)

Go to the different help sections:

General Information
Home Page
Navigation Panel
BLAST Search
Genome Browser
Gene Details
Comparative Alignment Viewer
Downloads
Statistics
Species Names Abbreviations

General Information

The DB-AT contains transcriptomes of Apicomplexa parasites, as well as datasets reflecting a diverse nature of the transcriptomes in individual parasites both in vivo and in vitro. Furthermore, the RNA-Seq data of 116 Indonesian malaria patients infected with Plasmodium falciparum are available. The data can be accessed and displayed through the Genome Browser and also downloaded from the Download pages. The database can be used to, e.g., study the interaction between apicomplexa parasites and their hosts, or obtain transcriptome information of the species of interest.

Note about name switch from Full-Malaria to DB-AT

Since the 2015 update of this database, the name was changed to "DB-AT -DataBase of Apicomplexa Transcriptomes", to better reflect many different types of currently deposited data. Previous releases were called "Full-Malaria - Malaria Full-Length cDNA Database" and "Full-Parasites - Database of Full-Length cDNAs of Apicomplexa parasites".

Information on species in the database

Information on which species are found in the database is available on the statistics page.


Home Page

The home page displays a phylogenetic tree of the Apicomplexa species for which data are provided in the DB-AT. By clicking on the name of a species, user gets directed to the respective species' Genome Browser.



The navigation panel displayed on the left side of the web page contains the following links:


BLAST Search

The BLAST Search can be used to locate a nucleotide or protein query in an Apicomplexa species of interest.

Submitting a Query

In the BLAST Search page you can select the Program and the Database you want to use and provide a query sequence. To start BLAST, click on "Submit Query".

The available BLAST programs are:

The Datasets available are: For further information on the data for the species in DB-AT, please refer to the Statistics page.

blast search

BLAST Search Results Page

Once the BLAST Search is finished, the user is redirected to the BLAST Search Result page. It contains the results of the BLAST run in the pairwise format (see here for information on this output format). Each line in the table of hits (A) represents a subject sequence from the database, which aligned to the query sequence. When you click on a sequence name in this table of hits (A), you are directed to the alignment of this hit (B). Each hit contains a link "Go to browser" (C) which opens a new tab displaying the Genome Browser at the position of the subject sequence.

blast search

Parameters for BLAST search

For both blastn and tblastn searches the results are filtered for those with an e-value<0.001. Other run parameters are used at their default values.


Genome Browser

The Genome Browser displays the genomic sequence, genes and additional data for a specific region of a species' genome. The user can select on of several "tracks" that are displayed along the genome and depict, e.g., transcriptomic data, such as assembled sequences from RNA-Seq, RNA-Seq read pileup, mapping of EST or full-length cDNA sequences, etc.

The Different Panes of the Genome Browser


  2. Genomic Position

    The Genomic Region displayed in the Genome Browser is given in the top row. When this value is modified and subsequently the user clicks the "Go" button, the Genome Browser jumps to the given location.

  3. Navigation Panel

    The Navigation Panel below the row with the Genomic Region can be used to modify the view of the Genome Browser. The radio buttons "Browse" and "Info" switch between two different modes of the Genome Browser. There can always be only one mode active at a time.

    • Browse: The user can click in one of the displayed tracks and slide the region to be displayed to the left and right. By clicking and dragging in the representation of the genome (1),
      the user can draw a rectangle that specifies the region into which the Browser zooms in.
    • Info.: The user can click on a rectangle depicting a gene in one of the displayed tracks and a context menu opens. This menu gives the Gene ID and a link to a reference databases'
      entry for this particular gene, as well as the link "Detail", which redirects the user to a page in DB-AT giving more information on this gene (see Detail page).

    The user can also change the size of the Genome Browser by entering a width (in pixels) and clicking on "Change size". Furthermore, it is possible to show or hide the item panel that is shown on the left hand side on top of the Tracks by selecting/deselecting the "Show item panel" checkbox.

  4. Genomic Region

    This panel contains a "zoomed out" representation of the genomic region the user is currently seeing. Indicated by a red rectangle is the sub-region that is displayed in the panels below. Below the rectangle, its genomic size is given. On top of the yellow bar, the coordinates (e.g. 1,000,000) indicate the location on a given chromosome. The coordinates of the sub-region are given at the bottom of this panel.

  5. Tracks Display

    This panel contains the different tracks, which are described in more detail below. When "Show item panel" in the Navigation Panel is selected, the names of the tracks are shown on top of the tracks on the left hand side. Numbers in the top right corner give the value of the y-axis.

  6. Selection of Tracks to Display

    This part shows the different tracks that can be displayed in the Genome Browser, organized by categories. All track categories are collapsed by default. When the user clicks on the plus button on the left side of a blue title bar, the available tracks are expanded. All tracks available within each category can be switched on and off to modify the content of the Genome Browser. For some of the tracks, their description serves also as a link to accessing the data behind them.

The Different Track Displays

In general, the Genome Browser displays genes and mapped ESTs or full-length cDNAs as rectangles, and gene expression information as histograms. Below, each type of Track Display will be described in more detail.

Gene/EST Tracks

Thick blocks represent coding sequences, with arrows indicating whether the gene is on the plus (">"), or minus DNA strand ("<"). Thin blocks depict untranslated sequences (UTRs) and the connecting lines between blocks represent introns. Below the genes, their identifier is given. While being in the "Info" mode of the Genome Browser, the user can click on a gene to open a context menu (see Navigation Panel/Info.).
There are two kinds of representations of genes. One shows the gene in yellow color, the other in shades of green. While the yellow color code represents genes for which the genome information is available, different shades of green represent genes assembled de novo and subsequently mapped to annotated sequences of the reference species. Depending on the mapping results, different shades of green are used to depict the gene (see here for more detail).

gene color
Note on Dark and Light Green Colors in Gene Tracks for Babesia Species

In the tracks of "Other Babesia", like e.g. ESTs and transcripts, the mapped sequences are displayed in light and dark green colors. The mapping was performed using tblastx and since some EST sequences did map only to some parts of the Babesia bovis genome, the mapping regions are indicated by dark green color, while the surrounding region is shown in light green color.

Comparative View Tracks

In the comparative view tracks, the homologous regions between a pair of species are displayed. It is available as a track for selected species only. This track can be used to examine evolutionary conservation of transcript sequences and proximal regions. For an explanation of the species name abbreviations used, please see the table below. Clicking on the track and following the link "Show alignment details in this region", takes the user to an overview of alignments to be displayed in the Comparative viewer. For each gene that is currently displayed in the Comparative View track of the Genome Browser there is one link to an alignment. For more information on the comparative viewer, click here.



Bulk Summary and Single Cell Tracks

Both bulk summary and single cell tracks display the results of mapping RNA-Seq tracks/other transcriptomic data to the genome. The summary tracks show divergence in the expression levels of each transcript in the given dataset. The histograms display the number of reads mapping to this region in different units:




When the "Browse" mode is active, the user can modify the scale of the y axis (e.g., from normal to log scale).

Malaria patients RNA-seq



Tracks to be displayed can be selected by the buttons of Patient ID or "Distribution". "Distribution" button shows the variance gene expression.

Transcriptome tracks

For some of the species, RNA-seq sequencing was performed and followed by transcriptome assembly. The assembled sequences can be viewed as a separate track in the Genome Browser. Same representation scheme as in genes/ESTs tracks is used. The expression information of the assembled transcripts can be viewed as a RNA-seq pileup track. Additionally, the predicted splice junctions are available as a track with arcs joining beginnings and ends of the junctions. Junction information was produced by the TopHat program.


Gene Details


  1. Comparative Alignment: link to "Comparative alignment viewer".
  2. Assembled cDNA
  3. Protein Analysis
  4. Sequences - nucleotide sequence and amino acid sequence, if available
  5. CDS annotation: InterProScan result.


Comparative Alignment Viewer

The comparative alignment viewer contains three sections: the graphical representation of the alignment, the information on the gene product and the alignment statistics. The user can also display the whole alignment, see "Alignment Statistics". All alignments available in this comparative alignment viewer were produced with tblastn.


Comparative alignment viewer

This viewer displays the alignment of a specific region between two species. The user can interactively explore the region and also see the color coded nucleotide composition.

Gene Product

A table gives the symbol for this gene and the name of its product for both of the compared species.

Alignment Statistics

Statistics of the tblastn alignment between the two species are shown here. To see the whole alignment, the user can click on "alignment details".


Download

In the Download section, users can access the data that are unique to DB-AT and also the genomic data from another database that was used for reference purpose. For almost all species, there are two folders present with available data. One labeled as "db-at" contains data unique to the DB-AT, while the other, labeled with the source database name (for example "PlasmoDB-11.0_Pfalciparum3D7"), contains data for a given species from the reference database. In the "db-at" folder, there are, if applicable, fasta, fastq and bam files from the different experiments that were performed. In the source database folder there are two files: a fasta file with the genome sequence and a GFF file with coordinates of the annotated genes. A list of all source databases is given in the Statistics page.

Statistics

The Statistics page contains information on the genome sizes of the different species, as well as the transcriptomic data that is found in DB-AT.

Species Names Abbreviations

The following abbreviations for species names were used:

Abbreviation Species
Pf Plasmodium falciparum
Pv Plasmodium vivax
Pb Plasmodium berghei
Py Plasmodium yoelii
Te/The Theileria equi
Tp Theileria parva
To Theileria orientalis
Bb Babesia bovis
Bo Babesia ovata
Tg Toxoplasma gondii
Nc Neospora caninum
Et Eimeria tenella
Em Eimeria maxima
Cp Cryptosporidium parvum