Top Tips

Top tip:

As a registered user, your past BLAST, ClustalW, and HMMER jobs will be saved and viewable on your user page if you are logged in. To see them go to the homepage, log in and then click on your name in the top right corner. Look for the "Your jobs" section with (bullet point) instructions for using the interface at the bottom.



Top tip:

New search engine at VectorBase

Searching via the box at the top of all pages now lets you find more than just genes! Most site content is now searchable.

Updated on February 2014: This tip and its image corresponds to the old (or Classic) VectorBase search. If you would like to learn how to use search in the new website please follow this link: www.vectorbase.org/tutorials/search. There you will find two tutorials, one for “Search” and one for “Advanced search”.

Top tip:

VectorBase Top Tip : Switch on a genome browser track via email It is now possible to send a link via email which will turn on a specified track in the recipient’s genome browser. This saves explaining to your colleagues and collaborators how to “Configure this page...”. Simply mouse-over the track name and then the chain-link icon in the popup. Then copy the URL (right mouse-click menu in most web browsers). Here is the (shortened) link from the graphic below (goo.gl/WL1pf) to prove that it works.

Updated on February 2014: The above tip corresponds to an older version of VectorBase genome browser. In the current version you can click on the share icon highlighted below.

Top tip:
  • Variant Effect Predictor
    Did you know you can predict the effect of variants within the vector genomes? A variant effect predictor is available through the ’Manage your data’ button found in the left hand navigation menu of the genome browser. Users can upload a text file containing the variation data in a tab-separated format (chromosome, start, end, allele, strand) and the predictor will return the consequence of this variation with information about the affected gene and transcript, any amino acid changes and whether this variation is currently in the database. Full documentation relating to both input and output file formats can be found at http://www.vectorbase.org/info/website/upload/var.html
    Top tip:
    • RSS feed
      Did you know that you can follow VectorBase news by subscribing to our RSS Feed? All news stories about the data and tools relevant to your research will automatically populate the feed as our team posts them. Subscribe in 5 secs. by clicking the ‘RSS Feed’ link at the bottom of the VectorBase home page and following the instructions on your web browser.
      Top tip:
      Did you know that VectorBase hosts several mailing lists? These range from the Newsletter recipient list, announcements to lists dedicated to specific species projects. We use the GUI mailman system and subscription is open to anyone. A detailed list of all mailing lists can be found on the Help Wiki.

      Updated on February 2014: There is only one mailing list to which you can subscribe, is called news@vectorbase.org. To subscribe (or unsubscribe) go to the Community tab and click on "Mailing list" as shown below.

      Top tip:

      Build your own Hidden Markov Model
      You can build a your own Hidden Markov Model based on a multiple alignment of your sequences using the online tool and then search VectorBase gene models for potential matches. You can find the HMMER tool in the Tools section at VectorBase.

      Updated on February 2014:If you would like to know more about how to find homolog sequences using Hmmer follow this link for a tutorial with a sample exercise, additionally we also have for you more sample files and practice exercises.

      Top tip:
      • Expanding ontology queries
        Did you know that when you perform a query in an ontology-based database this can be expanded to include all "is_a" children of the original query term? Thus, if when looking at the insecticide resistance data in VectorBase you are not certain about a specific term, you can search for a more generic term. All relevant results will then be displayed, even if districts and arrondissements are not part of the original record in the database.
        Top tip:

        Did you know you could add a comment to a gene?
        From the Gene Report page, in the Gene DAS Report section, click on “Add a comment”. You will need to have a VectorBase user account (so that comments and annotation submissions can be properly accredited). If you don’t already have an account, just sign up - it only takes a couple of minutes. Your comment will appear in the Gene DAS Report section.

        You can also use this system to associate gene descriptions, Gene Ontology terms and literature citations

        Updated on February 2014: This was only possible with the old (or classic) VectorBase.

        Top tip:

        Did you know how useful BioMart is?
        Perhaps you don't even know what BioMart is. Don't worry, we'll explain everything right here. First, do you need BioMart? Well, if you need information about more than a handful of genes or if you need to filter a large number of genes using some specific criterion, then the answer is yes. In fact, BioMart is exactly these two things (listing and filtering) and nothing else. VectorBase BioMart has just been updated for An. gambiae and Ae. aegypti so that you can list and filter most of the information shown in the genome browsers, such as genomic location, InterPro domains, signal peptides, Gene Ontology, microarray reporter IDs, orthologs etc. Come and try our BioMart – we’ve even written some examples of queries for you to try!

        Updated on February 2014: VectorBase BioMart has all our released genomes, except for Anopheles stephensi Indian, however we have A. stephensi SDA-500, which is the reference genome for this species. If you would like to know more about how to use BioMart for your queries, follow this link for a tutorial with a sample exercise, additionally we also have for you a sample file and more practice exercises.

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