VastDB release v1.1

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Published on 27 June 2018, 16:00 by Webadmin
VastDB has just been updated to version v1.1. We expect this version to be the first of several improvements to VastDB that will be implemented in the coming months.

The main updates with respect to v1.0 are:

  • First release of user-annotated biological functions of AS events: We have manually curated more than 300 biological functions supported by published research articles in PubMed, for human, mouse and chicken. Our Event view now shows these functions and the links to the articles in which they were described. Event functions are displayed both in the event in which they were originally described, and in all orthologous events. Our Gene View also shows the number of functions annotated for each event and its orthologues, to help users prioritise events within a gene. For examples, see gene ENSG00000004487@Genome:hg19 and event HsaEX0033219@Genome:hg19.
  • Improved coordinates for alternative splice site events: Each splice site in an event (e.g. HsaALTA0000001-1/2@Genome:hg19 and HsaALTA0000001-2/2@Genome:hg19, have now different genomic coordinates and sequences. For these events, A corresponds to the part of the exon with multiple splice sites that goes from the most proximal splice to the most distal splice site of the exon. C1 (for Alt3 events) or C2 (for Alt5) corresponds to the part of the exon that is included, regardless of the splice site used. This means that, by definition, the most proximal splice sites in the event (those with a lower index, e.g. HsaALTA0000001-1/2@Genome:hg19), have no A coordinates nor sequence, as the part of the exon being included is only the constant one, corresponding to C1 in this case.
  • Improved ORF impact descriptions: We have included ORF impact predictions for Alt3, Alt5 and intron retention events.
  • Updates in our front-end stack, and several bug fixes

Thank you for using our website, and we hope that you find it useful for your work. Please remember that we are always looking forward to receiving more annotations of biological functions of AS events from users, and we are available by email or on Twitter to receive feedback and give support to users.

Happy VastDBing,

The VastDB team.