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WU-BLAST Analysis of two Homologous Genes
 
   

Summary

In this tutorial we will see examples on parseblast output when applying to a WU-BLAST file. This perl script is included in the gff2aplot distribution. There are three basic aligment formats that can be generated from a blast file by parseblast.pl, but all three must produce the same plots by gff2aplot. We will also see the raw output from gff2aplot and how to customize it a little bit.

NOTE.- For the sake of clarity, we are going to use long names for the comand-line switches. See the command-line help if you prefer short names for those cases in which a short name is available.
Bitmaps for the examples were generated as PNGs (Portable Network Graphics). If your browser is not ready for such format yet, you can visualize the PDF or PS versions by clicking on the links below each snapshot. Links to customization files, log files, GFF input files and output PostScript figures, are also available on each command-line shown.

Contents


Parsing BLAST Output


    
$BIN/parseblast.pl --verbose --no-frame --aplot             \
                   -- taf6.mmhs.genomic.blastn              \
                    > taf6.mmhs.genomic.blastn.aplot.gff    \
                   2> taf6.mmhs.genomic.blastn.aplotgff.log
  

    
$BIN/parseblast.pl --verbose --no-frame            \
                   --fullgff --compact-tags        \
                   -- taf6.mmhs.genomic.blastn     \
                    > taf6.mmhs.genomic.blastn.gff \
                   2> taf6.mmhs.genomic.blastn.log
  

    
$BIN/parseblast.pl --verbose --no-frame --fullgff       \
                   -- taf6.mmhs.genomic.blastn          \
                    > taf6.mmhs.genomic.blastn.full.gff \
                   2> taf6.mmhs.genomic.blastn.full.log
  

    
$BIN/parseblast.pl --verbose --no-frame --aplot              \
                   -- taf6.mmhs.genomic.tblastx              \
                    > taf6.mmhs.genomic.tblastx.aplot.gff    \
                   2> taf6.mmhs.genomic.tblastx.aplotgff.log
  

Raw Output


Empty Plot
 [PNG] [PS] [PDF] 
    
gff2aplot.pl                        \
    --verbose                       \
    -- taf6.mmhs.genomic.blastn.gff \
       taf6.mm.gene.gff             \
       taf6.hs.gene.gff             \
     > taf6.mmhs.genomic.blastn.ps  \
    2> taf6.mmhs.genomic.blastn.log
  

Empty Plot
 [PNG] [PS] [PDF] 
    
gff2aplot.pl                              \
    --verbose                             \
    -- taf6.mmhs.genomic.blastn.aplot.gff \
       taf6.mm.gene.gff                   \
       taf6.hs.gene.gff                   \
     > taf6.mmhs.genomic.blastn.aplot.ps  \
    2> taf6.mmhs.genomic.blastn.aplot.log
  

Empty Plot
 [PNG] [PS] [PDF] 
    
gff2aplot.pl                               \
    --verbose                              \
    --show-percent-box                     \
    -- taf6.mmhs.genomic.tblastx.aplot.gff \
       taf6.mm.gene.gff                    \
       taf6.hs.gene.gff                    \
     > taf6.mmhs.genomic.tblastx.aplot.ps  \
    2> taf6.mmhs.genomic.tblastx.aplot.log
  

Modifying Plot Settings


Empty Plot
 [PNG] [PS] [PDF] 
    
gff2aplot.pl                                                    \
    --verbose                                                   \
    --title 'Hsap/Mmus taf6 Orthologous Gene'                   \
    --subtitle                                                  \
      'Figure displays BLASTN results for this genomic region.' \
    --show-percent-box                                          \
    --custom-filename taf6.tblastx.rc                           \
    -- taf6.mmhs.genomic.blastn.aplot.gff                       \
       taf6.mm.gene.gff                                         \
       taf6.hs.gene.gff                                         \
     > taf6.mmhs.genomic.blastn.aplot_conf.ps                   \
    2> taf6.mmhs.genomic.blastn.aplot_conf.log
  

Empty Plot
 [PNG] [PS] [PDF] 
    
gff2aplot.pl                                                     \
    --verbose                                                    \
    --title 'Hsap/Mmus taf6 Orthologous Gene'                    \
    --subtitle                                                   \
      'Figure displays TBLASTX results for this genomic region.' \
    --show-percent-box                                           \
    --custom-filename taf6.tblastx.rc                            \
    -- taf6.mmhs.genomic.tblastx.aplot.gff                       \
       taf6.mm.gene.gff                                          \
       taf6.hs.gene.gff                                          \
     > taf6.mmhs.genomic.tblastx.aplot_conf.ps                   \
    2> taf6.mmhs.genomic.tblastx.aplot_conf.log
  

Merging Data


Empty Plot
 [PNG] [PS] [PDF] 
    
gff2aplot.pl                                   \
    --verbose                                  \
    --title 'Hsap/Mmus taf6 Orthologous Gene'  \
    --subtitle                                 \
      'Merging BLASTN and TBLASTX alignments.' \
    --show-percent-box                         \
    --custom-filename taf6.tblastx.rc          \
    -- taf6.mmhs.genomic.blastn.aplot.gff      \
       taf6.mmhs.genomic.tblastx.aplot.gff     \
       taf6.mm.gene.gff                        \
       taf6.hs.gene.gff                        \
     > taf6.mmhs.genomic.blast.merge.ps        \
    2> taf6.mmhs.genomic.blast.merge.log
  

Empty Plot
 [PNG] [PS] [PDF] 
    
gff2aplot.pl                                                       \
    --verbose                                                      \
    --title 'Hsap/Mmus taf6 Orthologous Gene'                      \
    --subtitle                                                     \
      'BLASTN alignments shown in green, TBLASTX results in blue.' \
    --show-percent-box                                             \
    --custom-filename taf6.tblastx.rc                              \
    --source-var 'BLASTN::alignment_color=darkgreen'               \
    --source-var 'TBLASTX::alignment_color=darkblue'               \
    -- taf6.mmhs.genomic.blastn.aplot.gff                          \
       taf6.mmhs.genomic.tblastx.aplot.gff                         \
       taf6.mm.gene.gff                                            \
       taf6.hs.gene.gff                                            \
     > taf6.mmhs.genomic.blast.merge_conf.ps                       \
    2> taf6.mmhs.genomic.blast.merge_conf.log
  

  
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