Enjoy LSKB's Synonym and Relation Searches.

A New Type of Software for Analyzing Genomes and Genes

Private Data Management Software for Researchers

Determination of the Taxonomy and Indentification of Fungi and Bacteria Based on DNA Sequence Analyses.

Analysis Support Tool for Allele Frequency

Inferring of Species at the DNA Level

KIN is a database application that utilizes microorganism databases to classify and to identify unknown bacteria and fungi at the DNA sequence level. KIN's databases include sequences of ribosomal RNA (rRNA), which is highly conserved and has a moderate evolutionary rate. Furthermore, KIN's databases contain regions around rRNA. From the homologies of sequences stored in the database and the query sequence, first, homologous species are identified. Next, a multiple alignment using the selected sets of the identified genera is performed, and finally, a bootstrap analysis is conducted to construct a phylogenetic tree.

Highly Accurate Databases for 16S,18S,and ITS sequences

All the sequences stored in KIN are collected from public databases, and their annotations are filtered by text mining techniques. Finally, only highly accurate information are clustered and stored according to the NCBI's Taxonomy. The stored sequence information can be viewed at any time.
A query sequence can be classified to the family and genus level by performing a homology search to a database for 16S or 18S sequences. If the ITS sequence of a microorganism of interest is available, first, a sub database can be constructed from the results of the homology search using its 18S sequence. Then, the microorganism of interest can be classified by performing another homology search to the sub database using the ITS sequence. Through this stepwise process, a detailed evolutionary classification can be obtained readily.

List of Functions
Inferring of Species Through Homology Searches
KIN infers the species of the microorganism of your interest from the results of the homology search performed to the sequences of the known microorganisms stored in the database.
  • KIN is equipped with 16S rRNA (for bacteria), 18S rRNA, and ITS (Internal Transcribed Spacer, which exists between 18S and 26S) sequences (for fungi) collected and filtered from public databases.
  • In the case of a bacterium, a BLAST search is performed against the 16S rRNA database.
  • In the case of a fungus, a BLAST search is performed against the 18S rRNA database, followed by another BLAST search to the ITS database.
  • KIN accepts query sequences in the GenBank, EMBL, and FASTA formats.
  • KIN is equipped with an export function for BLAST results.
Performing Multiple Alignment Analyses and Creating Phylogenetic Trees
After a BLAST search, KIN performs a multiple alignment using selected groups of sequences that belong to the narrowed down families and genera from the BLAST search and the sequences selected from the BLAST results.
  • A multiple alignment can be performed against families and genera of your interest specified after a homology search.
  • Sequences can be added to the group of sequences and BLAST results for a multiple alignment.
  • A query sequence can be added or removed from a multiple alignment.
  • ClustalW is used as the multiple sequence alignment program.
  • Target sequences for the alignment can be filtered by Score and Identity.
  • The alignment results can be viewed as a phylogenetic tree (TreeView must be installed on your computer.)
Outputting and Saving of Data Sets
The BLAST and multiple alignment results can be outputted and saved.
  • The sequence data in the databases are classified and stored according to the NCBI's Taxonomy.
  • The sequence data can be outputted for each family and genus or selected sequence, and saved in the GenBank or FASTA format.
  • BLAST results can be saved.
  • Results of multiple alignments can be outputted in the HTML format.
  • Query sequences for a bootstrap can be exported in the text format.
  • Results of a bootstrap can be outputted in the php file format.
Hardware Requirements

OS : Windows 2000, XP
CPU : 1GB or more
Memory : 1GB or more
HDD : 500MB or more of disk space
Other : ClustalW and TreeView programs

Database Update

KIN's databases for homology searches will be updated periodically. For the first year, the fees for updates are included in the price for the software. However, additional charges are needed from the second year.


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