パッケージ: staden (2.0.0+b11-4)
DNA sequence assembly (Gap4/Gap5), editing and analysis tools
Staden is a fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin).
Gap4 performs sequence assembly, contig ordering based on read pair data, contig joining based on sequence comparisons, assembly checking, repeat searching, experiment suggestion, read pair analysis and contig editing. It has graphical views of contigs, templates, readings and traces which all scroll in register. Contig editor searches and experiment suggestion routines use confidence values to calculate the confidence of the consensus sequence and hence identify only places requiring visual trace inspection or extra data. The result is extremely rapid finishing and a consensus of known accuracy.
Pregap4 provides a graphical user interface to set up the processing required to prepare trace data for assembly or analysis, and automates these processes.
Trev is a rapid and flexible viewer and editor for ABI, ALF, SCF and ZTR trace files.
Prefinish analyses partially completed sequence assemblies and suggests the most efficient set of experiments to help finish the project.
Tracediff and hetscan automatically locate mutations by comparing trace data against reference traces. They annotate the mutations found ready for viewing in gap4.
Spin analyses nucleotide sequences to find genes, restriction sites, motifs, etc. It can perform translations, find open reading frames, count codons, etc. Many results are presented graphically and a sliding sequence window is linked to the graphics cursor. Spin also compares pairs of sequences in many ways. It has very rapid dot matrix analysis, global and local alignment algorithms, plus a sliding sequence window linked to the graphical plots. It can compare nucleic acid against nucleic acid, protein against protein, and protein against nucleic acid.
その他の staden 関連パッケージ
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- dep: libc6 (>= 2.17)
- GNU C ライブラリ: 共有ライブラリ
以下のパッケージによって提供される仮想パッケージでもあります: libc6-udeb
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- dep: libcurl3-gnutls (>= 7.16.2)
- 使いやすいクライアントサイドの URL 転送ライブラリ (GnuTLS フレーバ)
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- dep: libfontconfig1 (>= 2.12.6)
- 汎用フォント設定ライブラリ - ランタイム
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- dep: libfreetype6 (>= 2.2.1)
- FreeType 2 フォントエンジン共有ライブラリファイル
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- dep: libgcc1 (>= 1:3.0)
- GCC 共有ライブラリ
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- dep: liblzma5 (>= 5.1.1alpha+20120614)
- XZ 形式の圧縮ライブラリ
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- dep: libpng16-16 (>= 1.6.2-1)
- PNG ライブラリ - ランタイム (バージョン 1.6)
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- dep: libstaden-read13
- Staden library for reading and writing DNA sequencing results
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- dep: libstdc++6 (>= 5)
- GNU 標準 C++ ライブラリ v3
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- dep: libtcl8.6 (>= 8.6.0)
- Tcl (Tool Command Language) v8.6 - ランタイムライブラリファイル
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- dep: libtk8.6 (>= 8.6.0)
- Tk toolkit for Tcl and X11 v8.6 - run-time files
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- dep: libx11-6
- X11 クライアントサイドライブラリ
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- dep: libxext6
- X11 用の雑多な拡張ライブラリ
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- dep: libxft2 (>> 2.1.1)
- X 用の FreeType ベースのフォント描画ライブラリ
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- dep: libxss1
- X11 Screen Saver extension library
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- dep: staden-common (= 2.0.0+b11-4)
- Architecture independent files for Staden
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- dep: staden-io-lib-utils
- programs for manipulating DNA sequencing files
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- dep: tklib
- standard Tk Library
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- dep: zlib1g (>= 1:1.1.4)
- 圧縮ライブラリ - ランタイム
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- rec: med-config (>= 2.1)
- Debian Med general config package