Re: [Gmod-gbrowse] Medaka Browser

[Scott C. <sc...@sc...>]

Hi Carolina,

You've emailed the mailing list that supports people who install and
maintain GBrowse, the genome browser that medaka people are using.
Unfortunately, I don't know anything about the data in that GBrowse
instance, so I can't answer your questions. Did you try using their
"contact us" page at https://shigen.nig.ac.jp/medaka/strain/contactUs.jsp
?  I also found this email address that you might try:
nbr...@bi....

Good luck!
Scott


On Mon, Jun 26, 2023 at 8:55 AM Carolina Agostini <
car...@st...> wrote:

> Good morning,
>
> My name is Carolina Agostini and currently I am a master student at
> University of Trento (Italy). I have been working with medakafish for some
> years now and I had the chance to discover this very interesting website (
> http://medaka.nig.ac.jp/service/menu), in which we can look at different
> medaka strains genomes, or blast genes' sequences of interest.
>
> The problem is that I am having issues in understanding how the browser
> works. Therefore I would like to ask you some specific information.
>
>
>    1. For example, there is the chance to download the sequence of a
>    specific chromosome, but to which stain does it belong? There is no
>    information about that. Is it possible to download the sequences of a
>    chromosome only of the Kaga strain?
>    2. When I try to blast a gene sequence in the BLAST search I obtain a
>    list, clicking on the list I can reach the browser main page and decide
>    what to look at. On select tracks I can for example focus my research on
>    Kaga and HdrR strains alignments, obtaining the coverage of the gene. The
>    problem is that when I try to reduce the base pairs shown on the browser, I
>    am actually able to see nucleotide sequences, but I am not able to
>    understand if the gene sequence present in HdrR genome, is also present in
>    Kaga genome and if the sequence is actually the same of whether there are
>    differences (i.e. SNPs...).
>
>
> I really hope that I was able to correctly express myself, unluckily I am
> not a bioinformatician.
>
>
> I am looking forward to hear from you soon,
>
> Thank you in advance for your attention.
>
>
> Best regards,
>
> Carolina
>
> --
>
> Carolina Agostini, Master student
> Laboratory of Translational Neurogenetics
>
> Department of Cellular, Computational and Integrative Biology, CIBIO
>
> Università degli Studi di Trento
> <https://maps.google.com/?q=Trento+Via+Sommarive+9+38123+Trento-Povo+Italy&entry=gmail&source=g>
>
> Via Sommarive 9
> <https://maps.google.com/?q=Trento+Via+Sommarive+9+38123+Trento-Povo+Italy&entry=gmail&source=g>
>
> 38123 Trento-Povo
> <https://maps.google.com/?q=Trento+Via+Sommarive+9+38123+Trento-Povo+Italy&entry=gmail&source=g>
>
> Italy
> <https://maps.google.com/?q=Trento+Via+Sommarive+9+38123+Trento-Povo+Italy&entry=gmail&source=g>
>
>
>
> Tel.: (0039) 0461 283763
>
> Web
>
> www.cibio.unitn.it/744/laboratory-of-translational-neurogenetics
>
> https://mcarl255.wixsite.com/mysite
>
>
> _______________________________________________
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> Gmo...@li...
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>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott
at scottcain dot net
GMOD Project Manager (http://gmod.org/)
216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
Human Cancer Models Initiative Project Manager (
https://hcmi-searchable-catalog.nci.nih.gov/)