MedakaBase Manual

January 29, 2024

MedakaBase User Manual
Table of Contents:
1. Introduction
2. Gene Name Search
3. Genome Browser (JBrowse, WebApollo)
4. BLAST
5. GMAP - cDNA Alignment
6. Genome Slicer
7. Gene Fetcher
8. Download
9. Terms of Use
1. Introduction
In 2022, NBRP Medaka incorporated a new mission related to the dissemination of genomic
information into its activities involving organisms familiar to Japanese, Medaka. To launch
MedakaBase web server, Dr. Masaru Yagura, a former researcher of the NBRP project at theNational Institute of Genetics, Molecular Life History Laboratory, collaborated under thesupervision of Professor Yasukazu Nakamura, Genome Informatics Laboratory at the National
Institute of Genetics. Building on the experience of operating the Cats-I web server, MedakaBase
service was initiated at the end of 2022.
The primary mission of NBRP Medaka’s activities is to facilitate the sharing of existing
genomic resources rather than acquiring new ones. Consequently, a platform was established topromote the effective utilization of already available data in public databases, along withnavigation tools to facilitate user engagement. This document aims to clarify the various tools
provided by MedakaBase.
As of 2024, Dr. Kenji Morikami, a researcher at Molecular Life History Laboratory, isresponsible for maintaining and making improvements to the MedakaBase web server as needed,
to enhance user-friendliness.
Related Sites:
・Medaka-annex: https://github.com/Squalomix/medaka-annex
Compiles various Medaka-related sites, including MedakaBase.
・Medaka Shigen: https://shigen.nig.ac.jp/medaka/
Provides diverse and useful biological information about Medaka including sequence
information.
Latest Information:
The latest information about MedakaBase is announced in Medaka Omics News, mainly inJapanese, and systematic information about server operation, such as scheduled downtime formaintenance, is communicated through MedakaBase Twitter account.
Contact: nbrp.medaka.info@gmail.com(Kenji Morikami, Mana Sato, Shigehiro Kuraku)

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2. Gene Name Search https://medakabase.nbrp.jp/
Perform the gene name search from the top page of this site or by using the search window on
the right side of the menu bar.
The search is conducted against the gene names assigned to Medaka assembly in Ensembl
entries. Information from Ensembl entries is based on Ensembl Release 107 (July 2022; genebuild May 2018).

For tips on search techniques, please refer to the guide just below.
Depending on how gene names are specified, such as utilizing wildcards (*) it becomes
possible to search for multiple members of a gene family simultaneously.
*Caution*
As information retrieval across species is not supported, if search involving multiple species
simultaneously is required, please perform the search on the Ensembl website.

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3. Genome Browser
3.1. JBrowse https://medakabase.nbrp.jp/viewer/Hd-rR/
Choose items you want to view from the checkboxes listed on the left, and they will be displayedon the browser. From left lists, you can select gene models from Ensembl and/or NCBI, while
mapping RNA-seq reads available in public as BAM files. The displayed RNA-seq data issourced from the following papers; Ichikawa et al., Nat Comm 2017 , Pasquier et al., BMC
Genomics, 2016 , & Uchida et al. BMC Biol. 2022.
*Caution*
The gene models starting with “liftoff_” (available for HNI and HSOK) were generated by using
Liftoff by the NBRP Medaka Team. Please note that they are based on cross-species inference
and are not supported by endogenous evidence for the individual species.

The genome browser capable of displaying both NCBI and Ensembl gene models simultaneously
is exclusive to MedakaBase.
Furthermore, NBRP Medaka originally optimized GTF files (not GFF files) by extending UTRs
for advanced molecular analysis including single-cell analyses, and the files are now publicly
accessible here. However, display of the new gene model on this JBrowse is currently notsupported.
3.2. WebApollo
A tool that allows modification of the structure of gene models (e.g., start and end points ofexons). However, it is not in general use now.

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4. BLAST https://medakabase.nbrp.jp/tools/blast/Enter your own nucleotide or amino acid sequence into the box as the query and the sequence
type is automatically determined. Then, select either the nucleotide or protein database listed in
the lower section, and a similarity search will be performed. The discrimination of sequence typeis done automatically. Briefly, BLASTN is used for nucleotide vs. nucleotide, BLASTX fornucleotide vs. amino acid, TBLASTN for amino acid vs. nucleotide, and BLASTP for aminoacid vs. amino acid.
*Caution*
1) Please avoid selecting unnecessary databases, as it may prolong the analysis time. Keep theselection to the minimum necessary.
2) Please note that in the nuclear genome sequence of Oryzias latipes (Hd-rR strain), there arearound 900 sequences (unanchored contigs) that are not integrated into chromosomes and are notpart of the publicly available assembly. These sequences are included in the search targets of[Genome] in the Nucleotide databases. When hits are found in BLAST searches, they areexplicitly labeled as “unanchored contig”, distinct from chromosomes.

Interpretation
For detailed information about the BLAST program, NCBI provides guides. The search
results are displayed by ranking the similarity of sequences. However, it’s important to note that
BLAST is not a tool for determining that the sequences have the same ancestor (i.e., homology)
or for identifying the orthology. Especially for orthology determination, additional steps such as
drawing and adequately interpreting molecular phylogenetic trees are necessary.

4MedakaBase ManualNotes
As part of NBRP’s activities in 2023, the genome sequence of Oryzias mekongensis wascurated and added to the search target databases. Furthermore, the Molecular Life History
Laboratory has acquired the genome information of Pacific saury serving as one of the outgroups
closely related to the Oryzias genus. The assembly of Pacific saury is already accessible throughthe NCBI genome database and custom genome browser.
When presenting research results based on results from this web site, please not only
mention MedakaBase but also cite the origin of these sequences. For example, in the case ofOryzias celebensis, cite Ansai et al., Nat Comm 2021. For more details, please carefully read the“9. Terms of Use” mentioned later.

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5. GMAP - cDNA alignment https://medakabase.nbrp.jp/tools/gmap/
A tool for aligning your transcript sequences onto the genome, considering information about theintrons.
Input your sequence, such as cDNA, in the provided box, and choose the target species from the[Genome] popup menu, and then select the desired display format from the [Format] popupmenu. The mapping results will be displayed. When you download the file by clicking “Fulldocument” at the bottom, note that the file does not have any extensions, but you can open itwith a text editor.
Application
This tool allows mapping cDNA sequences to the genome while considering intron
information. By using this, it becomes possible to grasp, for example, the exon ends necessaryfor experimental design. Specifically, by selecting “only show alignment” at the bottom of the[Format] popup menu, you can accurately determine, at a 1bp level, where introns are inserted
into the cDNA sequence. Although the intron sequences are not displayed in this data, theinsertion positions of introns are indicated by numbers. Using these numbers, you can extract thenucleotide sequence with the Genome Slicer (refer to “6. Genome Slicer” described below). Thiscan be applied to easily design gRNA on introns, 5’UTRs, or 3’UTRs.

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6. Genome Slicer https://medakabase.nbrp.jp/tools/genome_slicer/
This tool allows you to cut and display a specific region of a genome sequence based on
specified coordinates (start to end) for a given ID.
To use, refer to the example provided in the lower section. Input the genome sequence ID(chromosome number) and define the start and end points. The term “Complement” in the“Example” section indicates the method for acquiring the complementary strand sequence. By
specifying numerical values in descending order, you can obtain the sequence of thecomplementary strand.

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7. Gene Fetcher https://medakabase.nbrp.jp/tools/gene_fetcher/This tool enables the extraction of specific regions of a gene.
Select the target organism from the [Genome] popup menu and choose the desired type ofsequence from “Gene sequence”. In the “Gene” section, select either FASTA or GenBankformat for the output. You can also specify numerical values in the empty fields next to “5’upstream/3’-downstream” to obtain the flanking sequence, including upstream and downstream
sequences of the target gene, based on the specified number of bases.
Enter the Gene ID of the target gene, which must be an Ensembl Transcript ID starting with“ENSORLT”, into the box.

The information for Ensembl entries is based on Ensembl Release 107 (July 2022; gene build
May 2018).

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8. Download https://medakabase.nbrp.jp/download/
You can obtain the sequences for the desired organism.
Select the target organism from the popup menu, and click on the file name. Determine the typeof sequence (Genome, CDS, or Protein) based on the file extensions.

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9. Terms of use
When reporting the research results based on output from MedakaBase, it is crucial not only tomention MedakaBase but also to cite the source of the sequence data. For example, in the case ofOryzias celebensis, please refer to the paper by Ansai et al., Nat Comm 2021.
The sources of information utilized in MedakaBase are shown on the TOP page as follows.
Information from Ensembl entries is based on Ensembl Release 107 (July 2022).
*Caution*
Regarding the sequence information for Oryzias mekongensis, as it is unpublished, please contact
NBRP Medaka Team (nbrp.medaka.info@gmail.com) for any inquiries related to its disclosure.

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