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Using Gbrowse for EST database


    SalmonDB uses Generic Genome Browser (Gbrowse) as the platform for information retrieval of EST collections from Salmo salar and Oncorhynchus mykiss. The interface is mainly graphical (see figure) and it is available from Tools menu and from every gene page.   


        The following figure shows a Contig sequence.  If you want to see which predicted SNPs are contained within this CDS, you should activate this track by selecting the appropiate checkbox, located in the track section at bottom of the image (not shown). Then, reload the image by pressing the corresponding button. With this action, the new image will show required information.

    To navigate to a genome region, use the Landmark or Region search box. Contig regions are designated by contig_id:start..end. From this track you can download fasta files for the active sequence and you can also design primers spawning a specific region within this sequence (See primer design).

    You can configure many things, such as which tracks are displayed and in what order. Tracks available for each contig are shown in the figure starting from the instructions track to end with the SNPs prediction track.

    You can hold the mouse button and drag it over a specific region within the unigene to zoom in or send it to Blast.

    An important feature of GBrowse is their graphical approach. You can navigate with the mouse pointer over the screen and when you stop at some track, a pop up will show a brief description about this particular result. The pop up layout depends on which type of information is being displayed. For blast results, if you click on it a pop up will illustrate the alignment between the unigene sequence and the corresponding blast hit.


    For non-blast tracks you can also click on them and you will be redirected to a detailed view.  For example, you can click on the CDS track and it will show its sequence, length and other features.

   

    Using Gbrowse for genomic database


    A very useful feature of the website is that you can use gbrowse to explore the genomes for non-salmonids aquaculture species described before. This is public data from ensembl databases. To simplify the graphical interface there are only four tracks available under detailed view in salmonDB, GC content, 6-frame translation, gene and mRNA track. If you need more detailed information about any region you can click on the corresponding track and you will be redirected to the ensembl database.


    The figure shows a region spawning 100kbp within chromosome 5. It contains 5 different genes with their respective mRNA prediction.