Metadata for staden in main

---
Type: desktop-application
ID: gap5.desktop
Package: staden
Name:
  C: gap5
Summary:
  C: Staden gap5 assembly editor
Description:
  C: |-
    <p>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.</p>
  en: |-
    <p>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.</p>
Categories:
- Biology
- Science
Icon:
  cached:
  - name: staden_icon4bl.jxl
    width: 64
    height: 64
Launchable:
  desktop-id:
  - gap5.desktop

---
Type: desktop-application
ID: gap4.desktop
Package: staden
Name:
  C: gap4
Summary:
  C: Staden gap4 assembly editor
Description:
  C: |-
    <p>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.</p>
  en: |-
    <p>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.</p>
Categories:
- Biology
- Science
Icon:
  cached:
  - name: staden_icon4bl.jxl
    width: 64
    height: 64
Launchable:
  desktop-id:
  - gap4.desktop

---
Type: desktop-application
ID: trev.desktop
Package: staden
Name:
  C: trev
Summary:
  C: Staden trev program
Description:
  C: |-
    <p>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.</p>
  en: |-
    <p>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.</p>
Categories:
- Biology
- Science
Icon:
  cached:
  - name: staden_icon4bl.jxl
    width: 64
    height: 64
Launchable:
  desktop-id:
  - trev.desktop

---
Type: desktop-application
ID: pregap4.desktop
Package: staden
Name:
  C: pregap4
Summary:
  C: Staden pregap4 DNA preprocessor
Description:
  C: |-
    <p>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.</p>
  en: |-
    <p>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.</p>
Categories:
- Biology
- Science
Icon:
  cached:
  - name: staden_icon4bl.jxl
    width: 64
    height: 64
Launchable:
  desktop-id:
  - pregap4.desktop