KAIKObase manual
Version 4
October 2020

Copyright @ National Agriculture and Food Research Organization (NARO). All Rights Reserved.

Outline
1 Introduction
2 Top page
2.1 Chromosome Overview
2.2 Keyword and Position Search
2.3 BLAST Search
2.4 Curated Genes
3 Description page
4 Genome browser
5 Contact

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11 Introduction
KAIKObase is a silkworm genome database with a genetic map viewer
and a genome viewer. The latest KAIKObase (version 4) was constructedbased on the chromosomal-level genome assembly released in 2019(10.1016/j.ibmb.2019.02.002) together with the genetic markers andold gene sets from the previous KAIKObase.
New updates in KAIKObase version 4 include that:
1.
2.

3.

New genome assembly is used as the reference genome in thegenome browser GBrowse.
16,880 new gene models (protein-coding genes) and 51,926
reference transcripts are added and accessible in the genome
browser. They are searchable in “BLAST search” and “Keywordsearch”.
Functional annotations of each new gene model and its expression
patterns in various tissues, as well as orthologs in closely related
lepidopterans and model vertebrate and insect organisms, areavailable in “description page”.

Old datasets kept in new KAIKObase include that:
1.
2.

Genetic markers (SNP markers, BAC-end sequences, and fingerprintcontigs) and scaffolds of old genome assembly are available on thebase of new genome assembly.
Old protein-coding gene sets (Gene set A, China gene model,FLcDNA, and EST) were mapped onto new genome and aresearchable in “BLAST search” and “Keyword search” and accessible
in genome browser.

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2 Top pageThe top page of KAIKObase contains the announcement about database
update and the data mining pages.
KAIKObase provides four data mining approaches as listed on the tabs:
1 Search from linkage and physical map in Chromosome Overview
2 Keyword and Position Search
3 BLAST Search against silkworm genome and gene sets
4 List of manually curated genes

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2.1 Chromosome Overview
Linkage and physical map of 28 chromosomes are provided. Click thenumber under the chromosome to see the genetic map. Detailed
information of genetic map will be described in the next page.

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Features of genetic map (UnifiedMap)
Specify zooming level
Select chromosome

Check items to display

Click and drag the frame to the region of interest
Red frame: linkage map
Blue frame: physical map

Linkage map (red frame)* Place mouse on marker to find the pop-up informationand link to physical map (if available)* Red arrow will show if clicking the link to physical map

Physical map (blue frame)* Place mouse on marker to find the pop-up informationand links to Gbrowse and sequence (if available)

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2.2 Keyword and Position Search
Genes of interest can be searched by
1. Keyword (Gene ID, annotation, etc.)
2. Chromosomal position of a given region
3. A combination of keyword and position
The data set “New gene model” is selected for searching by default.

The entries of the pull-down menu in “Search Field” are:• all (default) – applicable for all datasets• local ID – applicable for all data sets
• public ID – used in Gene set A• clone name – used in FLcDNA, EST• accession ID – used in FLcDNA, EST• description – applicable for all data sets but EST

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“Search Results” show the hits on each chromosome and the list of hits.
The pull-down menu provides links to genome browser and map viewer.

Chromosomal distribution of hitsLinks

Besides links to genome browser and map viewer (“UnifiedMap” in themenu), additional links are also provided as follows.
•••••

New gene model: description page
Gene set A: description page
China gene model: gene viewer*, KAIKO2DDB*FLcDNA: FLcDNA DB*
EST: EST DB**: link to old KAIKObase
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2.3 BLAST Search“BLAST Search” provides five programs to search against five data sets.
Blastn, tBlastn, tBlastx can be used to search against• Genome sequence• New gene model (nucleotide)• Reference transcript (nucleotide)
Blastp, Blastx can be used to search against• New gene model (amino acid)• Reference transcript (amino acid)

Select BLAST program and database

Parameters for BLAST search

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The information page with an URL to the result appears after submitting
sequence(s) to search.

Chromosomal distribution of hits

List of hits ordered by e-value

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9123The Search Result page provides several links:1 Results are summarized to the file “BLASTresult.zip” for download,including following two files:••result_rawdata.txt: BLAST result in format 0restult.txt: tab-delimited text file of the table below the Search
Result page2 Link to the graphic summary and alignment of BLAST result
The alignment page further provides BLASTresult_rawdata.zip(containing result_rawdata.txt) for download and links to genome
browser for each hit.
3 Links to genome browser (for all data sets) and gene description
page (only for New gene model)

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102.4 Curated Genes“Curated Genes” provides lists of manually curated genes for users.
Currently three types of genes were curated:
1. Detoxification-related genes
2. Silk production-related genes
3. Target genes of pesticides
Click the link to check the list of genes.

The curated genes are listed in each

2

1

3

“Predicted gene ID” shows the gene ID of New gene model in the same
chromosomal position. ID which ends with an “M” shows that the intronexon structure of the curated gene is different from that of the New genemodel.
The page of gene list provides links to:
1 Link to description page2 Link to genome browser
3 Links to related articles

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3 Description page“Description page” shows genetic information of each gene, including
chromosomal position, nucleotide and amino acid sequences, mostsimilar gene in nr database, corresponding gene(s) in old KAIKObase (ifany), functional domains and motifs, orthologs, and expression data inseveral tissues.
Here ”KWMTBOMO00006” is used as an example. The description pageshows “Overview” by default.

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The page of gene list provides links to:
1 Link to genome browser
2 Link to NCBI
3 Link(s) to description page of old KAIKObase
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“Annotation” shows the functional domains and motifs. Click the URL ofeach ID to check its detailed information.

“Orthologs” provides a list of theorthologs in 5 lepidopterans,
6 model insects, and human andmouse.
Click the URL of each accession tocheck its detailed information.

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“Expression” shows the expression data from 10 different
tissues/locations. Below the expression data of the gene model showsthe expression data of the alternative splicing isoforms (if any).
Click the Link of each alternative splicing isoform to check its position on
chromosome in genome browser.

Expression data of gene model

Expression data of splicing isoform

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“Expression (log conversion of TPMs)” shows the same expression dataas “Expression” page, but the TPM values in Y axis are shown with log10
conversion for better comparison between transcripts.
TPM value with an offset of 1 was used for log10 conversion to avoid
negative values.

Expression data of gene model(log10 conversion)

Expression data of splicing isoform(log10 conversion)

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4 Genome browser
The genome browser (GBrowse) is accessible from the top page. It canalso be accessed through links provided in description pages, BLAST
results, keyword search results, etc.
The genome browser contains three parts: 1. File; 2. Help; and 3.
browser and settings.
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1. File: A pull-down menu shows up when the pointer gets close.
Information within the region
shown below can be exported tovarious file format under the“Export as…” option

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2. Help: A pull-down menu shows up when the pointer gets close.
“Help with this browser” will show
tutorial about how to use Gbrowse.

The tutorial is also accessible through the following URL:
http://kaikobase.dna.affrc.go.jp/gbrowse2/general_help.html
3. browser and settings: “Tracks” shows different gene sets within
selected chromosomal region. Default gene sets are as shown here.
Select tracks to be shown

Search chromosome and region

Scroll/Zoom

Tracks“Scroll/Zoom” bottoms allow users to check the up- and down-stream
regions of of current region. The pull-down menu provides options
from “Show 100 bp” to “Show 1 Mbp” for the users to select theoptimal length of the region for viewing the genes.
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”Select Tracks” shows the available tracks. Besides the default gene sets,
the following data sets are also visible:••••

Genetic markers (finger print contigs, BAC-end sequences, SNPmarkers)
Assembly (scaffolds of old genome assembly)
Curated genes
Restriction sites

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5 Contact
If you have any question or find any problem about KAIKObase, pleasecontact us through the following email:
SGPwebmaster@ml.affrc.go.jp

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