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.png
    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.png
    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.png
    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.png
    width: 64
    height: 64
Launchable:
  desktop-id:
  - pregap4.desktop