KAIKObase
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KAIKObase

[How to use KAIKObase]
The latest update on KAIKObase (ver.3.2.2) is now available. [Modification history]

We would like to ask for your patience not to submit papers using unpublished full-length cDNA is used for Silkworm Genome Annotation until the publication of full-length cDNA paper or annotation paper. If you have any question regarding this regulation, please contact:

KAIKObase is an integrated silkworm genome database and data mining tool with 3 map browsers, 1 gene viewer, and 5 independent databases. more...
 
  • PGmap : physical map and genetic linkage map for each chromosome.
  • UnifiedMap : PGmap containing genome contigs, BAC-ends, fosmid-ends, and Fingerprint Contigs (FPC).
  • GBrowse : genome annotation viewer based on GBrowse developed by GMOD.
  • GeneViewer : gene information viewer based on the gene viewer of KAIKOGAAS.
  • Bombyx Trap DataBase : Bombyx gene function database by transgenic works using GAL4 system.
  • KAIKO 2DDB : proteomic data of various developmental stages and tissues of silkworm.
  • KAIKOGAAS : an automated annotation system for analysis of the silkworm genome.
  • full-length cDNA database : full length cDNA and Bombyx complete cDNA derived from public database.
  • EST database : unreleased EST sequences and Bombyx EST sequences derived from public database.

KAIKObase provides three data mining approaches.

  1. narrowing the range of data sets using PGmap or UnifiedMap of Chromosome Overview.
  2. Keyword and Position Search.
  3. Sequence Search using BLAST.

Chromosome Overview
Keyword and Position Search
Scaffold Sequence Search

Chromosome Overview

Two choices are available for the genome maps the PGmap can be accessed by clicking the chromosome number after clicking PGmap (colored pink) and the UnifiedMap by clicking the chromosome number after clicking UnifiedMap (colored green).

PGmap:
physical map and genetic linkage map for each chromosome.
UnifiedMap:
PGmap containing genome contigs, BAC-ends, fosmid-ends, and Fingerprint Contigs (FPC).

Remarks:
As the size of gap between adjacent scaffolds is unknown, we set an uniform space of 500 kbps between scaffolds.
The direction of a scaffold containing plural markers is defined, while the direction of a scaffold having only one marker cannot be determined and the original direction is used.