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Newsletter 10 (Oct 2010)

Release Date: 
October, 2010
News: 
  • Driving Biological Projects
    A few months ago, VectorBase invited proposals for Driving Biological Projects (DBPs), funded by NIH/NIAID, these projects should use high-throughput experimental technologies to functionally characterize the genome, proteome or metabolome of vector species.
    Two projects were selected:
    • Comparative neurotranscriptome of Aedes aegypti PDF
    • Physical reference maps for vector genome assembly PDF

    The data generated will be made available through VectorBase. The next call should be announced in about 14 months (Jan.2012).

  • Culex quinquefasciatus genome paper
    The paper relating the sequencing, annotation and analysis of the Culex quinquefasciatus genome has been published this month in Science (Arensburger et al., 2010). As well as giving an overview of the genome structure and of the gene content, it presents a comparison of the three mosquito genomes and shows that increase in Culex gene number is partially due to a gene family expansion. A companion paper (Bartholomay et al., 2010) describes Culex responses to infection by diverse pathogens, and compares these responses in the three mosquitoes.
    Data: 
    • Anopheles gambiae M & S (VB-2010-10)
      Genome browsers are now available. At the moment it only contains repeats and EST alignments. The next release (Dec.2010) will bring Genscan gene models and UniProt mapping. Gene sets built from An. gambiae PEST are currently being produced and should be released early 2011.
      An article published this month in Science (Lawniczak et al., 2010) details the analysis of the M and S forms and reports widespread and heterogeneous genomic divergence, suggesting a well advanced speciation process and raising a challenge in identifying genes critical to this initiation.
      In a parallel collaboration between Imperial College London and the Broad Institute, the M and S sequences were used to design a 400K Affymetrix SNP-array. This SNPchip was used to survey large population structure in an article from the same issue of Science (Neafsey et al., 2010).
      The latest An. gambiae PEST genome browser already features the 400K SNP locations used on the array and future releases (from Dec.2010) will contain the genotypes described in the paper. Further data sets will be incorporated as they become available as this array is being made publicly available by Affymetrix.
    • Link to external resources (VB-2010-10)
      Mosquito genes from all 3 species are now linked to a new external reference: the Insect immune-related gene and gene family resource, ImmunoDB. The mosquito genomes have also been masked with transposable elements from the transposable element database TEFam.
    Tools: 
    • Contact form
      A new contact form can be found on the main page under the " Communications" section. Why not use it to send us your comments about our website?
      • What do you like? or don’t like?
      • Which data types you would like to see?
      • Which tools you would like to use?
      • How to improve our service?
      • Or tell us anything else you have to say!

      Feel free to leave your email address if you'd like to receive a response from the VectorBase staff or leave that field blank to comment anonymously.

    • RSS feeds
      We are pleased to announce expanded RSS services, now accessible from the “Communication” section of the VectorBase home page. VectorBase RSS includes four new feeds, providing information on
      • Our presence at scientific gatherings,
      • Publications,
      • Releases, and
      • Job positions relevant to our user community. Subscribe to stay up to date on the latest VectorBase developments!

      If you want to post a job advert via our job RSS feed, please contact info@vectorbase.org.

    Community: 
    • Meetings
    • Workshops
    • Networks
      • Interaction data
        We are regularly asked why VectorBase do not show interaction data. The simple answer is that there aren’t that many publicly available. So if you have hold of some interaction data, whether within the host itself or between host and pathogen, please submit them to an interaction archive database, or even better, to the International Molecular Exchange Consortium (IMEx). We will then link to these resources and show your data!
      • South African IRBase node
        IRbase is now in use at the National Health Laboratory Service of South Africa (Dr. Lizette Koekemoer). The system is used to store, search, and map their own insecticide resistance data using a web interface for both end users and curators. Data will be transferred to the VectorBase public repository at a later point.
        Do you also have insecticide resistance data you would like to share publicly? No need to install IRBase locally – just contact us and we will let you know how to do so.
    Contact us: 

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    Top tip: 

    This feature is not longer available on VectorBase as of early 2016

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    Newsletter 11 (May 2011)

    Release Date: 
    May, 2011
    News: 
    • Funding Opportunity
      The NIAID-funded VectorBase invites research investigations called Driving Biological Projects (DBPs) from organizations housing experimental laboratories having expertise and knowledge in working with arthropod vectors of human pathogens. We anticipate making two awards of up to $600K each by April 1, 2012. A two page Letter of Intent (LOI) is due August 1, 2011. Full proposals will be solicited by invitation only, with a deadline of November 1, 2011. See the full solicitation from the VectorBase site and send questions to vector@nd.edu.
    • Anopheles Genomes Cluster
      Samples are now in sequencing at the Broad Institute for the NHGRI/NIAID-supported project, “Genome Analysis of Vectorial Capacity in Major Anopheles Vectors of Malaria Parasites”. VectorBase looks forward to working together with the Broad and members of the vector community to process and host these new genomes and their meta-data. Please visit VectorBase often for project information, updates, and data as they become available.
    Data: 
    • Rhodnius prolixus
      An early pre-release of the Rhodnius prolixus genome is available. This annotation includes: repeat masking, ESTs and RNA-seq transcriptome alignments, UniProt peptide alignments, Genscan based gene models and an transcriptome derived geneset. Further data sets will be added in the coming months with the expected pre-release of the first genebuild for the June release.
    • Glossina morsitans
      The genome of the Tsetse fly, Glossina morsitans morsitans, has been sequenced and assembled by the Wellcome Trust Sanger Institute. A pre-release of the assembly will be available in the June release. Like the Rhodnius pre-release this will contain alignments of transcriptome and peptide data and ab initio gene predictions.
    Tools: 
    • Next-generation RNA-seq
      VectorBase now contains next-generation transcriptome sequence data sets (RNA-seq). Over the past few releases we have added data from 9 Anopheline species available for querying via the BLAST server and as data tracks served to the Anopheles gambiae browser via DAS. Further, the genome browser is now capable of displaying community members’ own indexed BAM files for all species.

      As more data sets become available VectorBase will continue to make these available to the community. A major update for Aedes aegypti is due for the June release including 1.3 M Roche 454 reads and 41 M Illumina reads from the Short Read Archive (SRA). We encourage our communities to contact us early to discuss visualization of newer generation sequencing data sets through VectorBase including resequencing data.

    Community: 
    • Meetings
      • 7th Annual BioMalPar Conference, Biology and Pathology of the Malaria Parasite. EMBL Heidelberg, Germany 16-18th May 2011
      • 5th Annual Arthropod Genomics Symposium Arthropod Genomics 2011: Exploring Diversity, Relating Similarity. Kansas City, USA, June 9 - 12, 2011
      • Fifth International Meeting on "Molecular and Population Biology of Mosquitoes and Other Disease Vectors". Kolymbari, Crete, Greece, 24-30 July 2011
      • Workshops
      • Networks
    Contact us: 

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    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 image: 
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      Newsletter 12 (Nov 2011)

      Release Date: 
      November, 2011
      News: 
      • Genome projects approved
        VectorBase has been informed that the NIH/NIAID vector genome working group has approved two new projects. One will sequence the mite vector of scrub typhus, Leptotrombidium deliense, and provide additional genome and transcriptome sequencing of Ixodes scapularis and related ticks. The second will target genomes of 11 Simulium (black fly) species, including the major S. damnosum siblings, S. woodii, S. ochraceum and S. vittatum.
        Data: 
        • Pre-sites
          To provide faster access to upcoming genomes, we have recently introduced preliminary sites, called “pre-sites”. These contain preliminary gene annotations, transcriptome and proteome alignments and represent a snap shot of the annotation process at a given time. The rationales for presenting such data are to give more frequent updates on the annotation and to engage the community much earlier in the process. Releases are data-driven, rather than time-driven, and as such pre-sites, are updated independently of the bi-monthly release cycle. Because these data are preliminary, they are not archived and non-searchable. While we strongly encourage the community to use them, we advise not to rely on the identifiers, as these will not be tracked.
          To date, we have been providing pre-sites for two species: Rhodnius prolixus and Glossina morsitans.
          • Rhodnius prolixus pre-site
            The 0.5 gene set has been released for R. prolixus; it was built using the Ensembl annotation pipeline. It is accessible via the new Rhodnius prolixus species page. Additional features such as RNA-seq and protein similarities, ab initio predictions and EST-build genes are also available in the genome browser accessible from the species page.
          • Glossina morsitans pre-site
            The 0.5 gene set has been released for G. morsitans and is our first annotation using the MAKER pipeline (Cantarel et al., 2008), rather than the more traditional Ensembl pipeline. It is currently undergoing some analysis from the Glossina community so we only provide gene models via BLAST and the Glossina morsitans species page. We welcome any help from the community, so please contact us if you would like to be involved in the manual annotation process!
        Tools: 
        • Unified population data
          During the summer, VectorBase unveiled its “beta” population biology web resource. Our aim is to bring together all population-based studies (field or lab) into one database so that geographic, experimental, phenotypic and genotypic characteristics can be queried, analysed and visualised. For now, it is possible to browse the mosquito field samples that were originally made available in VectorBase’s IRBase and AgPopGenBase resources, along with 60 samples from the Neafsey et al. SNP-chip paper. Comments and suggestions from the community are welcome at any stage in the development of this resource.
        Community: 
        • Meetings
          • Attending TropMed Philly?
            Visit us in the exhibits area at the ASTMH 60th Annual Meeting in Philadelphia, December 4-8, 2011. Representatives of VectorBase will be part of a shared exhibit along with several other NIH/NIAID Bioinformatics Resource Centers. VectorBase representatives will answer questions, demo VectorBase, help with queries and distribute materials.
        • Workshops
          • VectorBase workshops
            Our staff will be running a 2-day VectorBase workshop at the Liverpool School of Tropical Medicine (Liverpool, UK) in November. This event is now fully subscribed, but we invite other labs and institutes to host VectorBase workshops. You are free to select the topics you would like us to cover. If you are interested, please contact us at info@vectorbase.org for more details.
        • Networks
        Contact us: 

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        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.

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        Newsletter 13 (Sep 2012)

        Release Date: 
        September, 2012
        News: 

        New website coming soon!

        The VectorBase developers have been busy creating a new website with improved search and navigation, as well as a more consistent look and feel. During the transition period of several months, both new and old sites will run in parallel. Your feedback is very welcome at any time.
        Data: 

        New data for Rhodnius prolixus

        An enhanced gene build for Rhodnius prolixus has been included as part of the VB-2012-04 release. The high number of trascripts has been reduced. At the present time, the following data are available: repeats, EST alignments, RNA-seq alignments, peptide alignments, full lenght cDNAs, Lagerblad gene models (clustered 454 sequences), consensus set with 16,122 genes and 16,134 trascripts, Genscan models, SNAP models, ncRNAs and pseudogenes. Note that VectorBase provides a BLAST service to compare your sequence against the R. prolixus supercontigs, trascripts and peptides.
        Tools: 

        VectorBase Expression Map

        VectorBase stores many high-throughput microarray (a.k.a. DNA chip) datasets which measure the relative amounts of thousands of Anopheles gambiae and Aedes aegypti gene product with respect to various experimental factors, such as tissues/organs, developmental stages and pathogens. Each experiment provides a wealth of information but, until now, a big picture "all genes, all factors" analysis has not been readly available. Such a holistic, or "systems", view of gene expression could greatly accelerate knowledge discovery and hypothesis generation from mosquito gene expression data. In our updated VectorBase Expression Map (MacCallum et al. 2011, BMC Genomics. Dec: 12:620) each A. gambiae and A. aegypti gene is assigned to one of 500 clusters. Because genes within a cluster have similar expression profiles, and the clusters are arranged on a rectangular grid, this resource is a powerful visualization tool for casual exploration and knowledge discovery. For example, we show in the figure below a query asking: Which genes are highly expressed in A. gambiae shortly after ingestion of a blood meal?

        Two regions of the map are highlighted in red. Examination of the clusters soon reveals that one region is dominated by high levels of expression in late embryonic development (green highlighting) and also genes involved in cuticle formation (yellow symbols). Thus in just a few minutes we can begin to hypothesize that one response to the blood meal is to remodel the cuticle in order to accomodate the large increse in volume. The map shows two further modes of behavior for cuticle genes: they are either constitutively expressed (in all experiments performed so far) or are expressed in the ovaries (blue highlighting).
        Community: 

        Outreach

        VectorBase workshops We invite labs and institutes to host VectorBase 1-2 day workshops. You are free to select the topics you would like us to cover. If you are interested, please contact us at info@vectorbase.org for more details.
        Contact us: 
        Post your comments, questions, suggestions or tweets! To (un)subscribe to the newsletter visit the Mailman admin page for this list.
        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 image: 
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        Newsletter 14 (Feb 2014)

        Release Date: 
        February, 2014
        Contact us: 
        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.



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        New Data: 

        28 genomes and counting

        We currently host 28 genomes and more are coming soon. For a complete list of our current species please visit www.vectorbase.org/genomes. In this page you can also check if either the assembly or gene set of your favorite organism has been updated.



        Our most recent updates include the genome of Biomphalaria glabrata, new assemblies for Aedes aegypti Liverpool, Anopheles stephensi Indian and A. darling Coari, and a new gene set for Glossina morsitans Yale.

        Anopheles 16 genomes project

        In September of 2008 funding was approved to sequence and assemble the genomes and transcriptomes of 13 Anopheles species. This project was inspired by very ambitious goals:

        • improved understanding of vectorial capacity
        • the application of that understanding toward reducing malaria disease burden

        An updated list of the 16 species that are now part of the project is available at https://olive.broadinstitute.org/projects/anopheles. Production sequencing began in spring 2011. Initial draft genome assemblies were finished in 2013. Transcriptome assemblies, genome assemblies, and gene models were recently "frozen" and variant discovery and community analysis started.

        All 16 reference genomes are inside VectorBase, and community gene annotation is now underway. More details about the project can be found in Neafsey et al 2013 following this link: http://www.ncbi.nlm.nih.gov/pubmed/23708298.

        Submit to VectorBase

        You are encouraged to contact us to:

        • Add transcript or protein data: This type of data can be displayed on the Expression Browser, Genome browser or Population Biology Browser (PopBio). Priority will be given to published (or about to be published) data submitted already in Ensembl, NCBI or the DDBJ.
        Outreach: 

        VectorBase Scientific User Group

        On February 3rd, 2014 we had our first (online) group meeting, please follow this link to meet the group members. The benefits and expectations for the user group are:

        • Learn about VectorBase's new data and new tools and resources, and provide feedback
        • Suggest new features and help test them
        • Provide input on outreach plans and opportunities

        Thank you very much to all the users that volunteer to particiapte in this group. Your input is very much appreciated.

        Callout for your pictures

        Do you want to share your pictures for our Images section? Go to https://www.vectorbase.org/image-gallery and look at what we have and what are we missing. If you would like to contribute and share your pictures free of copyright, please send us a link to your work. As with the other images, your name will be associated with each one of the pictures in VectorBase.

        Tutorials, practice exercises, sample files and videos

        Visit the page https://www.vectorbase.org/tutorials to learn how to better use VectorBase. If you are not very familiar with the page or need to show the basics to a new member in your lab, we recommend the "Tour" and "An overview of VB tools and resources".

        In our last release, VB-2013-12, we included practice excercises and sample files to make it easier for you to learn. More video tutorials will be incorporated this year, too. If you have any suggestions about topics not covered in the tutorials, please let us know.

        VectorBase Hands-on Workshop

        Are you attending the American Society of Tropical Medicine and Hygiene (ASTMH) 63rd Annual Meeting this year? If you are, please mark your calendars and extend your stay for a couple of extra nights: our next workshop will be before the meeting on Nov 1-2, 2014, in New Orleans, Louisiana, USA.

        The goal of the workshop is to present an overview of the VectorBase website and offer a training and data analysis opportunity. Seating will be limited to 30 people and priority will be given to scientists from disease-endemic countries. Previous VectorBase workshop attendees are not eligible. More details will come soon.





        Newsletter 1 (Sep 2007)

        Release Date: 
        September, 2007
        News: 
        • Launch of the Newsletter
          Welcome to the first issue of the VectorBase Newsletter. The newsletter highlights new data sets and tool developments available from VectorBase as well as giving advanced notice of upcoming changes. The newsletter will be sent quarterly to those subscribed to the newsletter@vectorbase.org mail list.
          Data: 
          • New identifiers for Anopheles
            We have changed the identifiers of genes, transcripts and proteins for Anopheles gambiae to bring them in line with the VectorBase nomenclature rather than that of Ensembl. For those of you who are familiar with the Drosophila gene identifiers you'll recognise the usage of -R/P suffixes for transcripts and proteins and alternative isoforms defined by a letter (e.g. -RA, -RB, -RC etc.). A major advantage of this system is that there is now an implicit connection between a gene and it's encoded transcripts and peptides as they all share the same identifier (AGAPxxxxxx).
          • Anopheles new gene set
            A new Anopheles gene set (AgamP3.4), was released in July containing approx. 12,000 protein-coding gene predictions. Manual appraisal of predictions on chromosome arm 2L has been completed and significant volumes of community annotation have been integrated. The VectorBase nomenclature for gene identifiers (AGAPxxxxxx) is employed throughout. Further details can be found on the VectorBase A.gambiae homepage.
            Please contact the VectorBase team if you have queries about this gene set. We are especially interested to hear from researchers who think we have deleted genes or made retrograde predictions for their favourite genes.
          • Ontology for Tick anatomy
            An application ontology covering the anatomy of ticks (TADS) has been developed in collaboration with Prof. Dan Sonenshine (Old Dominion University, USA). The TADS ontology, as well as the Mosquito anatomy ontology (TGMA), are now compliant with CARO (Common Anatomy Reference Ontology). These two Controlled Vocabularies (CVs), together with two additional ones covering the disease transmission physiology that are now under development, provide the basis for the annotation of gene expression experiments.
            All VectorBase-developed ontologies are available for browsing and download.
          • Tiling array
            A. gambiae tiling array data from Halasz et al (2006) is available as a DAS track on the genome browser (ContigView). This shows expression levels in adult male and female mosquitoes for 76,782 36-mer probes designed against exons from an old Ensembl gene set (release 15) and 94,469 probes targeted at regular intervals where there were no predicted genes. Enable the DAS track using the "DAS Sources" menu in the "Detailed view" (click on the box for "Tiling Expression") and then zoom out all the way (200Kb) to see the inter-gene probes. The 36-mer probes were designed to be unique. The mapping to the current repeat-masked VectorBase assembly used Exonerate in an ungapped alignment mode where only exact matches are shown.
          • Community Annotation Submission
            VectorBase will integrate community annotations into the canonical gene sets wherever possible. We have developed a submission interface for the community using a simple Excel spreadsheet form. Submitters will need to sign up for a VectorBase User account and can then proceed to submit gene predictions, CV terms, citations and general comments. Submissions are moderated by VectorBase community representatives and displayed using DAS. All submitted annotations will be integrated into the canonical set during a subsequent gene build.
          • Coming soon
            Two new gene sets are expected by the end of this year: the mosquito Culex pippins and the body louse Pediculus humans.
          Tools: 
          • Insecticide resistance ontology
            The insecticide resistance ontology is almost complete and will soon be available in VectorBase.
          Community: 
          • Meetings
          • Workshops
          • Networks
          Contact us: 

          To (un)subscribe to the newsletter visit the Mailman admin page for this list.

          Top tip: 

          Selecting regions Did you know you could use the mouse to draw a rectangular region on the genome browser windows and then zoom into that exact region. This is very useful when you want to focus on a particular feature (gene, exon, microarray probe, etc). It works in all the graphical display panels of ContigView.

          Updated on February 2014: If you go to the "Location Tab", in the Genome Browser, the "Region in Detail"(middle panel) will have a new icon called "switch to scrollable image". If you click on this icon three new features are available:

          • Scroll: navigate up or down in the chromosome or supercontig 5 Mb a the time. To update the bottom panel click on "update this image" or "Reset scrollable image".
          • Track height: certain tracks can be set to a fixed height of your choice, or to automatically expand or contract to fit all the features on the page.
          • Drag/Select: Using the mouse "Drag" or "Select" a region.
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          Newsletter 2 (Jan 2008)

          Release Date: 
          January, 2008
          News: 
          • Culex pipiens The genome of the mosquito Culex pipiens, vector of the West Nile Virus, has been sequenced and annotated and is now available at VectorBase. It complements the existing genomes of Anopheles gambiae and Aedes aegypti, completing the "mosquito triad", with one representative in each of the three main mosquito families being sequenced (Anopheline, Aedine and Culicine). The genome has been sequenced jointly by the Broad Institute and J. Craig Venter Institute (JCVI), and funded by NIAID. The shotgun sequencing was completed at the end of June 2006 and a first assembly of the 3,171 supercontigs, CpipJ1, has been produced by The Broad Institute using their whole genome assembly package ARACHNE. The 540 Mb assembly has been jointly annotated by the Broad Institute, JCVI and VectorBase. A total of 20,316 protein-coding genes were identified. Fasta files of the gene, transcript and protein sequences are available in the download section of VectorBase and the genome can be browse via our genome browser, with comparative data linking the three mosquito genomes.
          Data: 
          Tools: 
          • Genome De-linked Annotation Viewer
            As a result of feedback from within the community, we recognised a need for a method to disseminate annotation for species with data (e.g. EST sets) that lack genomic sequence. To meet this need, VectorBase has developed GDAV (Genome De-linked Annotation Viewer) - a lightweight web application which provides display and search facilities for sequence and text-based annotation.
            The first use of GDAV has been to publish the annotation of around 5,000 Anopheles albimanus ESTs at the Institute of Public Health, Mexico. This GDAV instance contains InterPro annotations and alignments to A. gambiae, A. aegypti and D. melanogaster.
          • HMMER Tools
            Providing multiple sequence alignments, the HMMER tools (HMMER Build & HMMER Search) create a probabilistic model that is then used to search the VectorBase databases. HMMER is similar to BLAST but is less likely to be affected by noise due to conservative or semi-conservative substitutions.
          Community: 
          • Meetings
          • Workshops
          • Networks
          Contact us: 

          To (un)subscribe to the newsletter visit the Mailman admin page for this list.

          Top tip: 

          Vizualising gene trees. Did you know that you could visualize the Gene Tree between a gene and its homologs? It is reachable from the left-hand tab of the geneview pages, under ‘gene tree info.’ The Gene Trees represent the evolutionary history of gene families. Red squares represent duplications nodes, blue squares represent speciation nodes. Clicking on an internal node gives a pop-up-menu with indications on its taxonomy and clicking on a gene gives its gene and protein IDs (linking to the cognate page), and various information. The green bars at the right of the tree are a schematic representation of the multiple alignment of the peptides made using MUSCLE. Full boxes indicate matches/mismatches, open boxes indicate gaps in the alignment.

          Updated on February 2014: It is reachable from the left-hand menu of the ‘Gene’ pages, under ‘gene tree (image).’

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          Newsletter 3 (Apr 2008)

          Release Date: 
          April, 2008
          News: 
          • Ixodes scapularis
            The genome of the blacklegged tick, a vector of Lyme disease, has been sequenced by the Broad Institute and the J. Craig Venter Institute (JCVI), and assembled by the latter into ~570,600 contigs and ~369,500 supercontigs. The assembly has an estimated 3.8X coverage of the genome and a total length of 1.8 Gb (including gaps). The contigs and supercontigs have been deposited in GenBank and are accessible at VectorBase.
          • Anopheles gambiae - M & S forms
            Two new molecular forms of Anopheles gambiae M and S, have been sequenced by the JCVI and the Washington University Genome Sequencing Center.
            Data: 
            • Ixodes scapularis
              The genome of the blacklegged tick, a vector of Lyme disease, has been sequenced by the Broad Institute and the J. Craig Venter Institute (JCVI), and assembled by the latter into ~570,600 contigs and ~369,500 supercontigs. The assembly has an estimated 3.8X coverage of the genome and a total length of 1.8 Gb (including gaps). The contigs and supercontigs have been deposited in GenBank [project ABJB010000000], and are accessible at VectorBase.
              A first annotation of the assembly is being undertaken by JCVI and VectorBase, and a preview of preliminary gene models, together with a genome browser for the assembly, will be available shortly at VectorBase.
              Interested members of the community are invited to sign-up for the Ixodes mailing list. and help us produce the first gene set for any chelicerate.
            • Anopheles gambiae
                M & S forms
                Two new molecular forms of Anopheles gambiae M and S, have been sequenced by the JCVI and the Washington University Genome Sequencing Center. Both assemblies and are accessible in GenBank [projects ABKP00000000 (M) and ABKQ00000000 (S)] and will soon be available at VectorBase.
              • Manual annotation
                Three chromosome arms: 2L, 2R and X, are now fully manually annotated. The annotation for 2L is visible as a DAS track in ContigView and the 2R and X will be visible soon. This manual annotation will be incorporated in the next revisions of the An. gambiae gene set.
            Tools: 
            Community: 
            • Meetings
            • Workshops
            • Networks
            Contact us: 

            To (un)subscribe to the newsletter visit the Mailman admin page for this list.

            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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            Newsletter 4 (Jul 2008)

            Release Date: 
            July, 2008
            News: 
            • Taxonomic change
              NCBI have changed the taxonomic name for Culex pipiens quinquefasciatus to simply Culex quinquefasciatus. Over the coming months VectorBase will be making this change on the website in line with the GenBank entries. The taxon identifier remains unchanged (7176).
              Data: 
              • Gene set update
                Manual appraisal of a subset of the initial Culex gene set has been undertaken and we were able to identify approximately 1,500 genes that appear to be mis-predicted. These predictions have been removed from the canonical gene set. The majority of the deleted genes were short (1 or 2 exons) and lacked clear orthologs with other species (both the mosquitoes and beyond) but had many paralogs within Culex.

                The new gene set, CpipiJ1.2, is available at VectorBase and has been submitted to GenBank. A list of the deleted genes is available on our website.

                We value input from the community; so if you spot a gene that you think should be deleted or corrected, please e-mail us and we will incorporate it into the next update.

              • Expression data resource

                The VectorBase gene expression resource (VBGE) continues to develop with a new user interface that makes finding and browsing experiments far easier and allows for the integration of Affymetrix data for the first time.
                A number of new data sets have been incorporated for Anopheles gambiae dealing with expression changes during blood meals and expression in adult tissue and larval gut compartments.
                You can access the data through the VBGE2.0 website by searching using gene or reporter names, and experiment descriptions. Links to expression summaries are available through the web browser, via the left hand navigation menu of a Gene Report page (see below).

              Community: 
              • Meetings
              • Workshops
              • Networks
              Contact us: 

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              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.

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              Newsletter 5 (Nov 2008)

              Release Date: 
              November, 2008
              News: 
              • VectorBase Forum
                Following several user requests we have set up a forum for the community to post conference announcements, job offers, ask questions or just discuss vectors and their genomes. The forum is open to anyone but posting message requires registration.
                Data: 
                • Insecticide Resistance
                  The insecticide resistance data section of VectorBase has been completely revamped! All the data are now annotated, stored, and searched using relevant ontologies (MIRO, GAZ). A new user interface based on AJAX is now availablei. Multiple criteria can be used to search the database and there is the option of exporting the results to a spreadsheet file. Mosquito collection sites with known coordinates have been also plotted on a map and the user can retrieve the corresponding assay data just by clicking on the collection site. Data submission can be done using either the online web interface or via a spreadsheet. Currently the database holds data for more than 1100 insecticide resistance assays from Africa and Asia. The WHO ANVR group will by using VectorBase as its repository for insecticide resistance data and a workshop took place in Senegal this month to train curators from 12 African countries.
                • Traces for blasting
                  For organisms without any genome available, such as the tsetse fly Glossina morsitans morsitans and the kissing bug Rhodnius prolixus, we are now offering the possibility to search against the traces (unassembled sequencing reads). So you can now do a Blast search against all the genomic data available for these vectors.
                Tools: 
                Community: 
                • Meetings
                • Workshops
                • Networks
                Contact us: 

                To (un)subscribe to the newsletter visit the Mailman admin page for this list.

                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 image: 
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