osfinder.dna.bio.keio.ac.jp

OSfinder - Home

OSfinder: A Tool for Accurate Orthology Mapping. Public release of OSfinder v1.4. Modify Perl scripts for drawing synteny maps. Public release of OSfinder v1.3. Modify merge algorithm so as to compute orthologous segment robustly. Public release of OSfinder v1.2. Add Perl scripts for automatically downloading genome sequence files from the NCBI GenBank database or protein sequence files from the Ensembl genome browser. Public release of OSfinder v1.1. Public release of OSfinder v1.0.

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OSfinder - Home | osfinder.dna.bio.keio.ac.jp Reviews

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OSfinder: A Tool for Accurate Orthology Mapping. Public release of OSfinder v1.4. Modify Perl scripts for drawing synteny maps. Public release of OSfinder v1.3. Modify merge algorithm so as to compute orthologous segment robustly. Public release of OSfinder v1.2. Add Perl scripts for automatically downloading genome sequence files from the NCBI GenBank database or protein sequence files from the Ensembl genome browser. Public release of OSfinder v1.1. Public release of OSfinder v1.0.

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OSfinder - Home | osfinder.dna.bio.keio.ac.jp Reviews

https://osfinder.dna.bio.keio.ac.jp

OSfinder: A Tool for Accurate Orthology Mapping. Public release of OSfinder v1.4. Modify Perl scripts for drawing synteny maps. Public release of OSfinder v1.3. Modify merge algorithm so as to compute orthologous segment robustly. Public release of OSfinder v1.2. Add Perl scripts for automatically downloading genome sequence files from the NCBI GenBank database or protein sequence files from the Ensembl genome browser. Public release of OSfinder v1.1. Public release of OSfinder v1.0.

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osfinder.dna.bio.keio.ac.jp

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OSfinder - From GenBank Data

http://osfinder.dna.bio.keio.ac.jp/ncbi.html

OSfinder: A Tool for Accurate Orthology Mapping. Make Input Files From GenBank Data. Step 0: Make Sure Requirements. Our Perl scripts for generating the input files of the OSfinder program require the following packages. The BioPerl module (1.5.2 or later version). Step 1: Get a list of organisms. First of all, type as follows in order to get a list of the organisms whose genome sequence files can be downloaded from the NCBI GenBank database. Cd osfinder v* */. Mode 0 - General mode. Mode 2 - Fungi mode.

2

OSfinder - To Do List

http://osfinder.dna.bio.keio.ac.jp/todo.html

OSfinder: A Tool for Accurate Orthology Mapping. Tasks that will be addressed in the near future. Increase the number of the anchor files that can be downloaded from the page "Mammalian Data". Implement a program that converts the results of OSfinder into the input of the MGR program. Which computes the reversal distance, in order to support the analyses regarding the genome rearrangement. In order to support the computation of whole genome alignments.

3

OSfinder - Make Input Files

http://osfinder.dna.bio.keio.ac.jp/input.html

OSfinder: A Tool for Accurate Orthology Mapping. Two approaches are commonly used for detecting anchors. The first approach detects homologous gene pairs between pairwise genomes, and considers the homologous gene pairs as anchors. The second approach detects short genomic sequences conserved among evolutionary related genomes, and considers the homologous sequences as anchors. Detect anchors based on your own strategy, and create the anchor files that have appropriate format. For details, click here.

4

OSfinder - File Format

http://osfinder.dna.bio.keio.ac.jp/format.html

OSfinder: A Tool for Accurate Orthology Mapping. Anchor File Format (Pairwise). The anchor files that can be accepted by the OSfinder program are composed by the lines, each of which corresponds to an anchor and has the following format. Chrom 1 start 1 end 1 sign 1 chrom 2 start 2 end 2 sign 2 [chrom i start i end i sign i] . Chrom 1", "chrom 2", and "chrom i" represent the chromosome IDs for the first, second, and i-th genome, respectively. Note that the chromosome IDs must be integer. 20 55496602 5549...

5

OSfinder - Publication

http://osfinder.dna.bio.keio.ac.jp/publication.html

OSfinder: A Tool for Accurate Orthology Mapping. Hachiya T, Osana Y, Popendorf K, Sakakibara Y. "Accurate Identification of Orthologous Segments among Multiple Genomes" (2009) Bioinformatics.

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Sakakibara Lab

http://www.dna.bio.keio.ac.jp/index.html

dna.bio.keio.ac.jp

Software - Sakakibara Lab

http://www.dna.bio.keio.ac.jp/software.html

Software - Sakakibara Lab. ゲノム配列から，アンカーと呼ばれる数十数百塩基程度の比較的短い相同領域を高速に検出するソフトウェアです 3 本以上の配列を同時に扱えることと，ヒトの染色体のような長い配列を扱えることが特徴です. Murasakiなどのゲノム比較ツールによって計算されたアンカーを入力としますそして，比較している生物種の中で，ゲノム再編成が起こっていない領域遺伝子の並びが変化していない領域を同定するプログラムです. RNA 配列のアラインメントと 2 次構造を計算するプログラムです 2 次構造未知の入力配列を 2 次構造既知の参照配列に対してアラインメントします. RNA 配列のアラインメントと 2 次構造を計算するプログラムです PHMMTS の拡張版であり，シュードノットと呼ばれる特殊な 2 次構造を扱うことができます. RNA 配列間の類似度を極めて正確に計算するプログラムですこれまでに機能性 RNA のファミリ予測，クラスタリング，プロファイル探索，相同性検索など様々な解析に応用され，いずれも世界最高の精度を達成しています (2010年11月現在).

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OSfinder - Home

OSfinder: A Tool for Accurate Orthology Mapping. Public release of OSfinder v1.4. Modify Perl scripts for drawing synteny maps. Public release of OSfinder v1.3. Modify merge algorithm so as to compute orthologous segment robustly. Public release of OSfinder v1.2. Add Perl scripts for automatically downloading genome sequence files from the NCBI GenBank database or protein sequence files from the Ensembl genome browser. Public release of OSfinder v1.1. Public release of OSfinder v1.0.

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