GFF2APLOT HOWTOs: Plotting WU-BLAST Results.
Author: Josep F. Abril
Description: GFF2APLOT HOWTOs: Analizing data from WU-BLAST alignment output.
Keywords: GFF2APLOT HOWTOs, tutorials, GFF, gff-format, Genomic Pairwise Alignments PostScript Plots, Genomic Analysis, Homology, Sinteny, Bioinformatics, WUBLAST

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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 WU-BLAST output. Raw `gff2aplot` output. Modifying plot settings. Merging alignment data.
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 |
[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
[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
[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 |
[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
[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 |
[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
[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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