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Re: [Gmod-gbrowse] Medaka Browser
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From: Kiyoshi N. <na...@ni...> - 2023-06-27 00:38:04
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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 基礎生物学研究所 バイオリソース研究室 （併任）総合研究大学院大学 生命科学研究科・基礎生物学専攻 成瀬 清 電話/ファクス: 0564-55-7580 (B15室） 0564-55-7554（301室） 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) email: na...@ni... 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