GCG Commands

 #DNA, RNA, タンパクなどの分子生物学的解析をする場合、頻繁に使用するコマンドを
    赤字(***, **)に、時々使うものを緑字(*)にしました。こうしてみると、コマンドと言っても、
    10〜15程度も知っていれば、ほとんど事足りてしまうことになりますね。 

各グループごとに、コマンドの機能を箇条書きにしてあります。知りたいグループの
表題をクリックしてください。

*******************************************************************

[Comparison]              [Database Searching] 

# Pairwise Comparison                 # Reference Searching        
      gap *                              lookup
     bestfit ***                        stringsearch **
     framealign                         names
     compare **
     dotplot**                      # Sequence Searching 
     gapshow                            blast **
                                         netblast
 # Multiple Comparison                  fetch **
      pileup *                          fasta **
      plotsimilarity *                    fasta_parsable_output
      pretty *                          tfasta **
      profileanalysis                     framesearch
      profilemake                         profilesearch
      profilegap                          profilesegments
      overlap *                           findpatterns
      nooverlap                         motifs **
      olddistances                      wordsearch **
                                        segments **

[Editing and Publication]       [Fragment Assembly] 

      seqed ***                           gelintroduction
      lineup                            gelstart *
      assemble                          gelenter *
      pretty                            gelmerge *
      publish                           gelassemble *
      plasmidmap                        gelview *
                                          geldisassemble

[Evolution]   [Gene Finding and Pattern Recognition] 

      paupsearch                          testcode
      paupdisplay                       codonpreference *
      distances                           frames
      growtree                            terminator
      diverge                           motifs *
                                          repeat
                                      findpatterns
[Mapping]                                composition
                                        codonfrequency *
      map ***                             correspond
      mapplot ***                         window
      mapsort *                           statplot
      fingerprint                         fitconsensus
      peptidemap *                        consensus
      plasmidmap                          xnu
      peptidesort **                      seg
 

[Importing and Exporting]        [Primer Selection]

      reformat **                       prime *
      breakup
      chopup
      fromstaden                    [Translation]
      fromembl*
      fromgenbank **                    translate ***
      frompir*                           backtranslate
      fromig                            map ***
      fromfasta                           extractpeptide
      tostaden                            pepdata
      topir
      toig
      tofasta
      getseq
      spew
 

[Protein Analysis]         [RNA Secondary Structure]

      motifs *                          mfold *
      profilescan                       plotfold *
      coilscan                          foldrna *
      hthscan                             squiggles
      spscan                              circles
      peptidesort **                      domes
      isoelectric                         mountains
      peptidemap *                      stemloop *
      pepplot *                         dotplot **
      peptidestructure *
      plotstructure *
      moment
      helicalwheel
      xnu
      seg
 

[Utilities]

 # Sequence Utilities                # File Utilities
      reverse **                          chopup
      shuffle                             replace
      simplify                            compresstext
      comptable                           onecase
      corrupt                             shiftover
      xnu                                 detab
      seg
      sample

 # Database Utilities                # Miscellaneous Utilities
      dataset                             setkeys
      gcgtoblast                        reformat **
      sample                              red
                                          name
 # Printing / Plotting Utilities          symbol
      lprint
      listfile
      setplot
      figure
      plottest
 
 


kmiura@@fujita-hu.ac.jp   (←@を一つ消してください)

Last update:03/07/2006