Metadata for staden in main

---
Type: desktop-application
ID: gap4.desktop
Package: staden
Name:
  C: gap4
Summary:
  C: Staden gap4 assembly editor
Description:
  da: |-
    <p>Staden er et fuldt udviklet sæt af DNA-sekvenssamling (Gap4 og Gap5), redigerings- og analyseværktøjer
    (Spin). Gap4 udfører sekvenssamling, contig-ordning baseret på læste pardata, contig-sammenslutning baseret
    på sekvenssammenligninger, kontrol af samling, gentag-søgning, eksperimentforslag, læst par-analyse og
    contig-redigering. Programmet har grafisk visning af contigs, skabeloner, læsninger og sporinger som
    alle ruller i register. Contig- redigeringsprogramsøgninger og forslagsrutiner for eksperimenter bruger
    konfidensværdier til at beregne konfidensen for konsensussekvens og identificerer dermed kun steder der
    kræver visuel sporingsinspektion eller ekstra data. Resultatet er ekstrem hurtig afslutning og en konsensus
    om kendt præcision. Pregap4 tilbyder en grafisk brugerflade til at opsætte behandlingen krævet for at
    forberede registreringsdata for samling eller analyse og automatiserer disse processer. Trev er en hurtig
    og fleksibel fremviser og redigeringsprogram for ABI-, ALF-, SCF- og ZTR-sporingsfiler. Prefinish analyserer
    delvise færdige sekvenssamlinger og foreslår det mest effektive sæt af eksperimenter til at hjælpe med
    at afslutte projektet. Tracediff og hetscan kan automatisk lokalisere mutationer ved at sammenligne sporingsdata
    mod referencesporinger. De annoterer mutationerne fundet klar til visning i gap4. Spin analyserer nukleotidsekvenser
    for at finde gener, begrænsningssider, motifs etc. Programmet kan udføre oversættelser, finde åbne læserammer,
    tælle codons etc. Mange resultater præsenteres grafisk og et glidende sekvensvindue er lænket til den
    grafiske markør. Spin sammenligner også sekvenspar på mange måder. Programmet har en meget hurtig punktmatrixanalyse,
    globale og lokale sammenligningsalgoritmer, samt et glidende sekvensvindue lænket til de grafiske plot.
    Programmet kan sammenligne nukleotidsyre mod nukleotidsyre, protein mod protein samt protein mod nukleotidsyre.</p>
  it: |-
    <p>Staden è un insieme completamente sviluppato di strumenti per assemblaggio (Gap4 e Gap5), modifica
    e analisi di sequenze di DNA. Gap4 effettua l&apos;assemblaggio di sequenze, l&apos;ordinamento di contigui
    basato su dati di coppie di letture, l&apos;unione di contigui basata sul confronto di sequenze, il controllo
    di assemblaggi, la ricerca di sequenze ripetute, il suggerimento di esperimenti, l&apos;analisi di coppie
    di letture e la modifica di contigui. Ha viste grafiche di contigui, modelli, letture e tracce, tutte
    con scorrimento nel registro. Le funzioni di suggerimento di esperimenti e le ricerche dell&apos;editor
    di contigui usano valori di confidenza per calcolare la confidenza della sequenza di consenso e perciò
    identificare solamente le posizioni che richiedono l&apos;ispezione visiva delle tracce o dati aggiuntivi.
    Il risultato è un tempo estremamente rapido e un consenso di accuratezza nota. Pregap4 fornisce un&apos;interfaccia
    utente grafica per impostare l&apos;elaborazione necessaria per preparare dati di tracce per l&apos;assemblaggio
    o l&apos;analisi e automatizza questi processi. Trev è un visualizzatore e un editor rapido e flessibile
    per file di traccia ABI, ALF, SCF e ZTR. Prefinish analizza assemblaggi di sequenze parzialmente completi
    e suggerisce l&apos;insieme più efficiente di esperimenti per aiutare a completare il progetto. Tracediff
    e hetscan localizzano automaticamente mutazioni confrontando dati di tracce con tracce di riferimento.
    Annotano le mutazioni trovate in modo che siano pronte per la visualizzazione in gap4. Spin analizza
    sequenze di nucleotidi per trovare geni, siti di restrizione, motivi, ecc. Può effettuare traduzioni,
    trovare frame di lettura aperti, contare i codoni, ecc. Molti risultati sono presentati graficamente
    e una finestra per sequenza con scorrimento è collegata al cursore grafico. Spin inoltre confronta coppie
    di sequenze in molti modi. Ha un&apos;analisi a matrice di punti molto veloce, algoritmi di allineamento
    globale e locale più una finestra per sequenza con scorrimento collegata ai tracciati grafici. Può confrontare
    acidi nucleici con acidi nucleici, proteine con proteine e proteine con acidi nucleici.</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>
  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>
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:
  da: |-
    <p>Staden er et fuldt udviklet sæt af DNA-sekvenssamling (Gap4 og Gap5), redigerings- og analyseværktøjer
    (Spin). Gap4 udfører sekvenssamling, contig-ordning baseret på læste pardata, contig-sammenslutning baseret
    på sekvenssammenligninger, kontrol af samling, gentag-søgning, eksperimentforslag, læst par-analyse og
    contig-redigering. Programmet har grafisk visning af contigs, skabeloner, læsninger og sporinger som
    alle ruller i register. Contig- redigeringsprogramsøgninger og forslagsrutiner for eksperimenter bruger
    konfidensværdier til at beregne konfidensen for konsensussekvens og identificerer dermed kun steder der
    kræver visuel sporingsinspektion eller ekstra data. Resultatet er ekstrem hurtig afslutning og en konsensus
    om kendt præcision. Pregap4 tilbyder en grafisk brugerflade til at opsætte behandlingen krævet for at
    forberede registreringsdata for samling eller analyse og automatiserer disse processer. Trev er en hurtig
    og fleksibel fremviser og redigeringsprogram for ABI-, ALF-, SCF- og ZTR-sporingsfiler. Prefinish analyserer
    delvise færdige sekvenssamlinger og foreslår det mest effektive sæt af eksperimenter til at hjælpe med
    at afslutte projektet. Tracediff og hetscan kan automatisk lokalisere mutationer ved at sammenligne sporingsdata
    mod referencesporinger. De annoterer mutationerne fundet klar til visning i gap4. Spin analyserer nukleotidsekvenser
    for at finde gener, begrænsningssider, motifs etc. Programmet kan udføre oversættelser, finde åbne læserammer,
    tælle codons etc. Mange resultater præsenteres grafisk og et glidende sekvensvindue er lænket til den
    grafiske markør. Spin sammenligner også sekvenspar på mange måder. Programmet har en meget hurtig punktmatrixanalyse,
    globale og lokale sammenligningsalgoritmer, samt et glidende sekvensvindue lænket til de grafiske plot.
    Programmet kan sammenligne nukleotidsyre mod nukleotidsyre, protein mod protein samt protein mod nukleotidsyre.</p>
  it: |-
    <p>Staden è un insieme completamente sviluppato di strumenti per assemblaggio (Gap4 e Gap5), modifica
    e analisi di sequenze di DNA. Gap4 effettua l&apos;assemblaggio di sequenze, l&apos;ordinamento di contigui
    basato su dati di coppie di letture, l&apos;unione di contigui basata sul confronto di sequenze, il controllo
    di assemblaggi, la ricerca di sequenze ripetute, il suggerimento di esperimenti, l&apos;analisi di coppie
    di letture e la modifica di contigui. Ha viste grafiche di contigui, modelli, letture e tracce, tutte
    con scorrimento nel registro. Le funzioni di suggerimento di esperimenti e le ricerche dell&apos;editor
    di contigui usano valori di confidenza per calcolare la confidenza della sequenza di consenso e perciò
    identificare solamente le posizioni che richiedono l&apos;ispezione visiva delle tracce o dati aggiuntivi.
    Il risultato è un tempo estremamente rapido e un consenso di accuratezza nota. Pregap4 fornisce un&apos;interfaccia
    utente grafica per impostare l&apos;elaborazione necessaria per preparare dati di tracce per l&apos;assemblaggio
    o l&apos;analisi e automatizza questi processi. Trev è un visualizzatore e un editor rapido e flessibile
    per file di traccia ABI, ALF, SCF e ZTR. Prefinish analizza assemblaggi di sequenze parzialmente completi
    e suggerisce l&apos;insieme più efficiente di esperimenti per aiutare a completare il progetto. Tracediff
    e hetscan localizzano automaticamente mutazioni confrontando dati di tracce con tracce di riferimento.
    Annotano le mutazioni trovate in modo che siano pronte per la visualizzazione in gap4. Spin analizza
    sequenze di nucleotidi per trovare geni, siti di restrizione, motivi, ecc. Può effettuare traduzioni,
    trovare frame di lettura aperti, contare i codoni, ecc. Molti risultati sono presentati graficamente
    e una finestra per sequenza con scorrimento è collegata al cursore grafico. Spin inoltre confronta coppie
    di sequenze in molti modi. Ha un&apos;analisi a matrice di punti molto veloce, algoritmi di allineamento
    globale e locale più una finestra per sequenza con scorrimento collegata ai tracciati grafici. Può confrontare
    acidi nucleici con acidi nucleici, proteine con proteine e proteine con acidi nucleici.</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>
  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>
Categories:
- Biology
- Science
Icon:
  cached:
  - name: staden_icon4bl.jxl
    width: 64
    height: 64
Launchable:
  desktop-id:
  - trev.desktop

---
Type: desktop-application
ID: gap5.desktop
Package: staden
Name:
  C: gap5
Summary:
  C: Staden gap5 assembly editor
Description:
  da: |-
    <p>Staden er et fuldt udviklet sæt af DNA-sekvenssamling (Gap4 og Gap5), redigerings- og analyseværktøjer
    (Spin). Gap4 udfører sekvenssamling, contig-ordning baseret på læste pardata, contig-sammenslutning baseret
    på sekvenssammenligninger, kontrol af samling, gentag-søgning, eksperimentforslag, læst par-analyse og
    contig-redigering. Programmet har grafisk visning af contigs, skabeloner, læsninger og sporinger som
    alle ruller i register. Contig- redigeringsprogramsøgninger og forslagsrutiner for eksperimenter bruger
    konfidensværdier til at beregne konfidensen for konsensussekvens og identificerer dermed kun steder der
    kræver visuel sporingsinspektion eller ekstra data. Resultatet er ekstrem hurtig afslutning og en konsensus
    om kendt præcision. Pregap4 tilbyder en grafisk brugerflade til at opsætte behandlingen krævet for at
    forberede registreringsdata for samling eller analyse og automatiserer disse processer. Trev er en hurtig
    og fleksibel fremviser og redigeringsprogram for ABI-, ALF-, SCF- og ZTR-sporingsfiler. Prefinish analyserer
    delvise færdige sekvenssamlinger og foreslår det mest effektive sæt af eksperimenter til at hjælpe med
    at afslutte projektet. Tracediff og hetscan kan automatisk lokalisere mutationer ved at sammenligne sporingsdata
    mod referencesporinger. De annoterer mutationerne fundet klar til visning i gap4. Spin analyserer nukleotidsekvenser
    for at finde gener, begrænsningssider, motifs etc. Programmet kan udføre oversættelser, finde åbne læserammer,
    tælle codons etc. Mange resultater præsenteres grafisk og et glidende sekvensvindue er lænket til den
    grafiske markør. Spin sammenligner også sekvenspar på mange måder. Programmet har en meget hurtig punktmatrixanalyse,
    globale og lokale sammenligningsalgoritmer, samt et glidende sekvensvindue lænket til de grafiske plot.
    Programmet kan sammenligne nukleotidsyre mod nukleotidsyre, protein mod protein samt protein mod nukleotidsyre.</p>
  it: |-
    <p>Staden è un insieme completamente sviluppato di strumenti per assemblaggio (Gap4 e Gap5), modifica
    e analisi di sequenze di DNA. Gap4 effettua l&apos;assemblaggio di sequenze, l&apos;ordinamento di contigui
    basato su dati di coppie di letture, l&apos;unione di contigui basata sul confronto di sequenze, il controllo
    di assemblaggi, la ricerca di sequenze ripetute, il suggerimento di esperimenti, l&apos;analisi di coppie
    di letture e la modifica di contigui. Ha viste grafiche di contigui, modelli, letture e tracce, tutte
    con scorrimento nel registro. Le funzioni di suggerimento di esperimenti e le ricerche dell&apos;editor
    di contigui usano valori di confidenza per calcolare la confidenza della sequenza di consenso e perciò
    identificare solamente le posizioni che richiedono l&apos;ispezione visiva delle tracce o dati aggiuntivi.
    Il risultato è un tempo estremamente rapido e un consenso di accuratezza nota. Pregap4 fornisce un&apos;interfaccia
    utente grafica per impostare l&apos;elaborazione necessaria per preparare dati di tracce per l&apos;assemblaggio
    o l&apos;analisi e automatizza questi processi. Trev è un visualizzatore e un editor rapido e flessibile
    per file di traccia ABI, ALF, SCF e ZTR. Prefinish analizza assemblaggi di sequenze parzialmente completi
    e suggerisce l&apos;insieme più efficiente di esperimenti per aiutare a completare il progetto. Tracediff
    e hetscan localizzano automaticamente mutazioni confrontando dati di tracce con tracce di riferimento.
    Annotano le mutazioni trovate in modo che siano pronte per la visualizzazione in gap4. Spin analizza
    sequenze di nucleotidi per trovare geni, siti di restrizione, motivi, ecc. Può effettuare traduzioni,
    trovare frame di lettura aperti, contare i codoni, ecc. Molti risultati sono presentati graficamente
    e una finestra per sequenza con scorrimento è collegata al cursore grafico. Spin inoltre confronta coppie
    di sequenze in molti modi. Ha un&apos;analisi a matrice di punti molto veloce, algoritmi di allineamento
    globale e locale più una finestra per sequenza con scorrimento collegata ai tracciati grafici. Può confrontare
    acidi nucleici con acidi nucleici, proteine con proteine e proteine con acidi nucleici.</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>
  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>
Categories:
- Biology
- Science
Icon:
  cached:
  - name: staden_icon4bl.jxl
    width: 64
    height: 64
Launchable:
  desktop-id:
  - gap5.desktop

---
Type: desktop-application
ID: pregap4.desktop
Package: staden
Name:
  C: pregap4
Summary:
  C: Staden pregap4 DNA preprocessor
Description:
  da: |-
    <p>Staden er et fuldt udviklet sæt af DNA-sekvenssamling (Gap4 og Gap5), redigerings- og analyseværktøjer
    (Spin). Gap4 udfører sekvenssamling, contig-ordning baseret på læste pardata, contig-sammenslutning baseret
    på sekvenssammenligninger, kontrol af samling, gentag-søgning, eksperimentforslag, læst par-analyse og
    contig-redigering. Programmet har grafisk visning af contigs, skabeloner, læsninger og sporinger som
    alle ruller i register. Contig- redigeringsprogramsøgninger og forslagsrutiner for eksperimenter bruger
    konfidensværdier til at beregne konfidensen for konsensussekvens og identificerer dermed kun steder der
    kræver visuel sporingsinspektion eller ekstra data. Resultatet er ekstrem hurtig afslutning og en konsensus
    om kendt præcision. Pregap4 tilbyder en grafisk brugerflade til at opsætte behandlingen krævet for at
    forberede registreringsdata for samling eller analyse og automatiserer disse processer. Trev er en hurtig
    og fleksibel fremviser og redigeringsprogram for ABI-, ALF-, SCF- og ZTR-sporingsfiler. Prefinish analyserer
    delvise færdige sekvenssamlinger og foreslår det mest effektive sæt af eksperimenter til at hjælpe med
    at afslutte projektet. Tracediff og hetscan kan automatisk lokalisere mutationer ved at sammenligne sporingsdata
    mod referencesporinger. De annoterer mutationerne fundet klar til visning i gap4. Spin analyserer nukleotidsekvenser
    for at finde gener, begrænsningssider, motifs etc. Programmet kan udføre oversættelser, finde åbne læserammer,
    tælle codons etc. Mange resultater præsenteres grafisk og et glidende sekvensvindue er lænket til den
    grafiske markør. Spin sammenligner også sekvenspar på mange måder. Programmet har en meget hurtig punktmatrixanalyse,
    globale og lokale sammenligningsalgoritmer, samt et glidende sekvensvindue lænket til de grafiske plot.
    Programmet kan sammenligne nukleotidsyre mod nukleotidsyre, protein mod protein samt protein mod nukleotidsyre.</p>
  it: |-
    <p>Staden è un insieme completamente sviluppato di strumenti per assemblaggio (Gap4 e Gap5), modifica
    e analisi di sequenze di DNA. Gap4 effettua l&apos;assemblaggio di sequenze, l&apos;ordinamento di contigui
    basato su dati di coppie di letture, l&apos;unione di contigui basata sul confronto di sequenze, il controllo
    di assemblaggi, la ricerca di sequenze ripetute, il suggerimento di esperimenti, l&apos;analisi di coppie
    di letture e la modifica di contigui. Ha viste grafiche di contigui, modelli, letture e tracce, tutte
    con scorrimento nel registro. Le funzioni di suggerimento di esperimenti e le ricerche dell&apos;editor
    di contigui usano valori di confidenza per calcolare la confidenza della sequenza di consenso e perciò
    identificare solamente le posizioni che richiedono l&apos;ispezione visiva delle tracce o dati aggiuntivi.
    Il risultato è un tempo estremamente rapido e un consenso di accuratezza nota. Pregap4 fornisce un&apos;interfaccia
    utente grafica per impostare l&apos;elaborazione necessaria per preparare dati di tracce per l&apos;assemblaggio
    o l&apos;analisi e automatizza questi processi. Trev è un visualizzatore e un editor rapido e flessibile
    per file di traccia ABI, ALF, SCF e ZTR. Prefinish analizza assemblaggi di sequenze parzialmente completi
    e suggerisce l&apos;insieme più efficiente di esperimenti per aiutare a completare il progetto. Tracediff
    e hetscan localizzano automaticamente mutazioni confrontando dati di tracce con tracce di riferimento.
    Annotano le mutazioni trovate in modo che siano pronte per la visualizzazione in gap4. Spin analizza
    sequenze di nucleotidi per trovare geni, siti di restrizione, motivi, ecc. Può effettuare traduzioni,
    trovare frame di lettura aperti, contare i codoni, ecc. Molti risultati sono presentati graficamente
    e una finestra per sequenza con scorrimento è collegata al cursore grafico. Spin inoltre confronta coppie
    di sequenze in molti modi. Ha un&apos;analisi a matrice di punti molto veloce, algoritmi di allineamento
    globale e locale più una finestra per sequenza con scorrimento collegata ai tracciati grafici. Può confrontare
    acidi nucleici con acidi nucleici, proteine con proteine e proteine con acidi nucleici.</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>
  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>
Categories:
- Biology
- Science
Icon:
  cached:
  - name: staden_icon4bl.jxl
    width: 64
    height: 64
Launchable:
  desktop-id:
  - pregap4.desktop