DEP-11 metadata for staden in xenial

---
Categories:
  - Biology
Description:
  C: <p>Staden is a fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis
    tools (Spin).</p><p>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.</p><p>Pregap4 provides a graphical user interface to set up the processing required
    to prepare trace data for assembly or analysis, and automates these processes.</p><p>Trev is a rapid
    and flexible viewer and editor for ABI, ALF, SCF and ZTR trace files.</p><p>Prefinish analyses partially
    completed sequence assemblies and suggests the most efficient set of experiments to help finish the
    project.</p><p>Tracediff and hetscan automatically locate mutations by comparing trace data against
    reference traces. They annotate the mutations found ready for viewing in gap4.</p><p>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.</p>
ID: pregap4.desktop
Icon:
  cached: staden_icon4bl.png
Name:
  C: pregap4
Package: staden
Summary:
  C: Staden pregap4 DNA preprocessor
Type: desktop-app

---
Categories:
  - Biology
Description:
  C: <p>Staden is a fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis
    tools (Spin).</p><p>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.</p><p>Pregap4 provides a graphical user interface to set up the processing required
    to prepare trace data for assembly or analysis, and automates these processes.</p><p>Trev is a rapid
    and flexible viewer and editor for ABI, ALF, SCF and ZTR trace files.</p><p>Prefinish analyses partially
    completed sequence assemblies and suggests the most efficient set of experiments to help finish the
    project.</p><p>Tracediff and hetscan automatically locate mutations by comparing trace data against
    reference traces. They annotate the mutations found ready for viewing in gap4.</p><p>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.</p>
ID: gap5.desktop
Icon:
  cached: staden_icon4bl.png
Name:
  C: gap5
Package: staden
Summary:
  C: Staden gap5 assembly editor
Type: desktop-app

---
Categories:
  - Biology
Description:
  C: <p>Staden is a fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis
    tools (Spin).</p><p>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.</p><p>Pregap4 provides a graphical user interface to set up the processing required
    to prepare trace data for assembly or analysis, and automates these processes.</p><p>Trev is a rapid
    and flexible viewer and editor for ABI, ALF, SCF and ZTR trace files.</p><p>Prefinish analyses partially
    completed sequence assemblies and suggests the most efficient set of experiments to help finish the
    project.</p><p>Tracediff and hetscan automatically locate mutations by comparing trace data against
    reference traces. They annotate the mutations found ready for viewing in gap4.</p><p>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.</p>
ID: trev.desktop
Icon:
  cached: staden_icon4bl.png
Name:
  C: trev
Package: staden
Summary:
  C: Staden trev program
Type: desktop-app

---
Categories:
  - Biology
Description:
  C: <p>Staden is a fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis
    tools (Spin).</p><p>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.</p><p>Pregap4 provides a graphical user interface to set up the processing required
    to prepare trace data for assembly or analysis, and automates these processes.</p><p>Trev is a rapid
    and flexible viewer and editor for ABI, ALF, SCF and ZTR trace files.</p><p>Prefinish analyses partially
    completed sequence assemblies and suggests the most efficient set of experiments to help finish the
    project.</p><p>Tracediff and hetscan automatically locate mutations by comparing trace data against
    reference traces. They annotate the mutations found ready for viewing in gap4.</p><p>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.</p>
ID: gap4.desktop
Icon:
  cached: staden_icon4bl.png
Name:
  C: gap4
Package: staden
Summary:
  C: Staden gap4 assembly editor
Type: desktop-app