[Gmod-gbrowse] Medaka Browser

[Carolina A. <car...@st...>]

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
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Web

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