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Guide to Comparative Genomics

In functions of comparative genomics, more than two closely related genomes are compared.

  • Implemented Software: 
  • Functions:
    • Drawing a Circular Genome Map
    • Multiple Genome Alignment
    • Dot Plot
    • VENN Diagram
    • Global Genome Rearrangement Map
    • Local Genome Rearrangement Map
    • EC Number Corresponding List
    • Metagenome Analysis using 16SrRNA Short Reads
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IMC O11 コアゲノム解析

There are no translations available.

  • この機能は以下のソフトウェアに搭載されています
    • IMCGE
    • IMCAE
    • GenomeTraveler
  • コアゲノム解析は、複数の近縁種ゲノム間での保存されたコア遺伝子を同定する機能です。以下は、3つのゲノム間のコア遺伝子を抽出し、並べたものです。
  • 相同遺伝子間のマルチプルアラインメントを表示できます。

より詳しく

IMC O10 遺伝子クラスターアラインメント

There are no translations available.

  • この機能は以下のソフトウェアに搭載されています
    • IMCGE
    • IMCAE
    • GenomeTraveler
  • 遺伝子クラスター解析は、複数の近縁種ゲノム上の同種遺伝子クラスターの並び方を図示する機能です。以下のように相同遺伝子間が直線で結ばれます。
  • より詳しく

IMC O02 多重リニアゲノムマップ

There are no translations available.

  • この機能は以下のソフトウェアに搭載されています
    • IMCGE
    • IMCAE
    • GenomeTraveler
  • 多重線状ゲノムマップ(Multiple Linear Genome Map)は、近縁種間の複数のゲノム染色体からのFeatureを並列に比較描画する機能です。
  • 多重線状ゲノムマップ上の1つフィーチャーを右クリックすることにより、他のゲノム上の全フィーチャーに対するホモロジー検索を実行でき、そのフィーチャーが他のゲノム上に相同な藩列を持つ場合は、相同遺伝子を軸にアライメント表示できます。
  • 多重線状マップからマウス右クリックで「IMC O10 遺伝子クラスターアライメント」を実行することができます。
  • PDF, PNG, EMFの各画像フォーマットでファイル出力できます。

より詳しく

O09 16SrRNA Metagenome Analysis

  • This function can be performed using the following software.
    • IMCGE
    • IMCAE
    • GenomeTraveler
  • Counting 16SrRNA reads that are derived from metagenome samples, show shares and frequencies of the reads in six ranks of the taxonomy tree.
  • Up to 24 metagenome samples can be analyzed.
  • Results can be saved as files and referred and viewed later.
  • Charts are printable and saved as image files.
  • The summing up results are saved as CSV files.
  • As for the 16SrRNA reference data, some of the existing databases can be registered and selected to be referred.
For further information.

O07 Drawing a local genome rearrangement map

Detecting homologous regions of a closely related whole genome against a basis whole genome, whole alignments of their nucleotide sequence level, amino acid sequence level and feature level are shown in the IMC feature map. This function is called "Local Genome Rearrangement Map: LGRM".

  • This function can be performed in the following softeare.
    • IMCGE
    • IMCAE
    • GenomeTraveler
  • Generate a local genome rearrangement map along the whole genome region between two closely related genomes.
  • The whole genome region of a compared genome is mapped against the whole region of the basis genome.
  • All the homology regions between two genomes are displayed in nucleotide sequence level.
  • On the coding regions, corresponding amino acid sequences are also displayed.
  • List up the variant bases amino acid residues and on click one of the variants brings to the corresponding region of the feature map.
  • Focusing on mutation sites on or upstream of a specified feature key.
  • All the features of the both genomes in the homologous regions are aligned graphically.
  • A result of the analysis is saved as a GenBank file with LGRM lane and can be reloaded.
  • A LGRM settings are saved as one of the layout styles (LGRM lane).
  • The display of Nucleotide sequence and amino acid sequence can be suppressed when the bases or residues of the both genome is accordance.
  • The LGRM lane can be printed with the feature map or saved as an image file.
  • The LGRM sequence lane can be saved as a file.
For further information.

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