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Alignment viewer
[example 1] alignments of >2 sequences
| scaffolds | references | tblastx | blastn |
|---|---|---|---|
| OBV_N00001 + OBV_N00003 | Cyanophage P-RSM6 | tblastx | blastn |
| OBV_N00002 + OBV_N00007 | Synechococcus phage S-SM2 | tblastx | blastn |
| OBV_N00005 + OBV_N00006 | Pelagibacter phage HTVC008M | tblastx | blastn |
[example 2] alignments of 2 sequences
| scaffold | reference | tblastx | blastn |
|---|---|---|---|
| OBV_N00003 | Cyanophage P-RSM6 | tblastx | blastn |
| OBV_N00005 | Pelagibacter phage HTVC008M | tblastx | blastn |
| OBV_N00006 | Pelagibacter phage HTVC008M | tblastx | blastn |
| OBV_N00020 | Synechococcus phage S-CBS2 | tblastx | blastn |
| OBV_N00023 | Cellulophaga phage phi38:1 | tblastx | blastn |
| OBV_N00024 | Cellulophaga phage phi38:1 | tblastx | blastn |
| OBV_N00025 | Cellulophaga phage phi38:1 | tblastx | blastn |
| OBV_N00041 | Puniceispirillum phage HMO-2011 | tblastx | blastn |
| OBV_N00044 | Puniceispirillum phage HMO-2011 | tblastx | blastn |
| OBV_N00046 | Puniceispirillum phage HMO-2011 | tblastx | blastn |
| OBV_N00073 | Pelagibacter phage HTVC019P | tblastx | blastn |
| OBV_N00080 | Klebsiella phage JD001 | tblastx | blastn |
| OBV_N00085 | Ralstonia phage RSB2 | tblastx | blastn |
| OBV_N00103 | Pseudomonas phage phiIBB-PAA2 | tblastx | blastn |
| OBV_N00113 | Sulfitobacter phage pCB2047-A | tblastx | blastn |
| OBV_N00119 | Persicivirga phage P12024L | tblastx | blastn |
| OBV_N00126 | Dunaliella viridis virus SI2 | tblastx | blastn |
| OBV_N00127 | Dunaliella viridis virus SI2 | tblastx | blastn |
| OBV_N00129 | Marinomonas phage P12026 | tblastx | blastn |
| OBV_N00135 | Persicivirga phage P12024L | tblastx | blastn |
| OBV_N00145 | Dunaliella viridis virus SI2 | tblastx | blastn |
| OBV_N00179 | Pelagibacter phage HTVC019P | tblastx | blastn |
Parameters
| name | description | default | example |
|---|---|---|---|
| autopos | Genomic position is automatically adjusted by centering the max score alignment ('on'), by the max length alignment ('length'), by the max alignment identity ('identity'), or no adjustment ('off') |
on | https://www.genome.jp/tools/mg_viewer2/aln/NC_016656/NC_020865?autopos=off |
| vertical | Part of blast result band is vertically displayed ('on') or parallelogram ('off') | off | https://www.genome.jp/tools/mg_viewer2/aln/NC_016656/NC_020865?autopos=on&vertical=on |
| scale | Number of nucleotides, which one pixel includes in alignments | 10 | https://www.genome.jp/tools/mg_viewer2/aln/NC_016656/NC_020865?scale=30 |
| tick_span | Span of long tick in alignemnt | 1000 | https://www.genome.jp/tools/mg_viewer2/aln/NC_016656/NC_020865?tick_span=5000 |
| grid_span | Span of grid in dot plot | 10000 | https://www.genome.jp/tools/mg_viewer2/aln/NC_016656/NC_020865?grid_span=20000 |
| show_labels | Gene labels are shown ('on') or not shown ('off') | on | https://www.genome.jp/tools/mg_viewer2/aln/NC_016656/NC_020865?show_labels=off&scale=50 |
| w_colorbar | Width of colorbar | 600 | https://www.genome.jp/tools/mg_viewer2/aln/NC_016656/NC_020865?w_colorbar=1000 |
| program | Program used for visualize: tblastx ('tblastx') or blastn ('blastn'). if multiple alignments are shown, 'n'th alignment can be configured by program'n'. e.g.) program1=blastn |
tblastx | https://www.genome.jp/tools/mg_viewer2/aln/NC_016656/NC_020865/NC_020867?program2=blastn&autopos=identity |
| cutpos | Each sequence is split by 'cutpos' and exchange the order of two fragment. This parameter is effective only when autopos is 'off'. 'n'th sequence can be configured by cutpos'n'. e.g.) cutpos1=10000 |
0 | https://www.genome.jp/tools/mg_viewer2/aln/NC_016656/NC_020865?autopos=off&cutpos1=10000 |
| strand | Each sequence is displayed in forward ('forward') or reverse ('reverse'). This parameter is effective only when autopos is 'off'. 'n'th sequence can be configured by strand'n'. e.g.) strand1=reverse |
forward | https://www.genome.jp/tools/mg_viewer2/aln/NC_016656/NC_020865?autopos=off&strand1=reverse |
| offset | Each sequence is displayed with left offset. Length can be given by number of nucleotides. This parameter is effective only when autopos is 'off'. 'n'th sequence can be configured by offset'n'. e.g.) offset1=3000 |
0 | https://www.genome.jp/tools/mg_viewer2/aln/NC_016656/NC_020865?autopos=off&offset1=3000 |