Re: [Gmod-gbrowse] Medaka Browser

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Dear Dr. Naruse,
Thank you very much for your prompt response. Please also thank Dr. Toyoda for
his help.
I understand that I cannot download the target sequence from the browser
and I will speak with my supervisor about mapping the reads myself.
Anyway, thank you both for all your suggestions.

I wish you all a nice week ahead.

With kind regards,
Carolina

Il giorno mar 27 giu 2023 alle ore 01:34 Kiyoshi Naruse <na...@ni...>
ha scritto:

> Dear Carolina and Scott,
>
> I asked Dr. Toyoda to download the target sequence from our browser. This
> feature is not implemented.
>
> 1. Reference sequence is the previous version (based on Sanger sequence)
> but not the current version (based on PacBio sequence and it will be more
> accurate).  It is better to update the reference sequence for your analysis.
> 2. Illumina short read data are public domain. You can use these data
> without our permission for your research, so I suggest you map these
> Illumina reads by yourself. This is an uncomplicated process using Bowtie
> or other mapping software.  You can make consensus sequence using these
> data too.
> Our Illumina reads data are as follows. Simple blast search using the consensus
> sequence will be work for your purpose.
> https://ddbj.nig.ac.jp/resource/sra-study/DRP000619
> Project name is "Whole genome sequencing of 5 medaka strains".
>
> Best wishes
> Kiyoshi
>
>
> 2023年6月27日(火) 1:05 Scott Cain <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
>>>
>>>
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> 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/)
>>
>> --
>> このグループから退会し、グループからのメールの配信を停止するには nbr...@bi...
>> にメールを送信してください。
>>
>
>
> --
>
>
> 〒444-8585　愛知県岡崎市明大寺町字西郷中38番地
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>
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>
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> email: na...@ni...
> Kiyoshi NARUSE, PhD
> National Institute for Basic Biology,
> Laboratory of Bioresources,
> Nishigonaka 38, Myodaiji, Okazaki 444-8585, Aichi,  Japan
> TEL/FAX: 0564-55-7580　(B15) 0564-55-7554 (301)
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>
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>
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>
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>
>

-- 

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