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Column descriptions
| Column | Description |
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| align_bp | RNA base pair relative to alignpos. |
| alignpos | Position in alignment. |
| color2_b | Foreground color, red component. |
| color2_g | Foreground color, green component. |
| color2_r | Foreground color, blue component. |
| color_b | Background color, red component. |
| color_g | Background color, green component. |
| color_r | Background color, blue component. |
| intron/exon | `.' unspecified. `I' intron. `E' exon. `?' unknown/ambiguous. |
| label | Type of info in this position. `N' is nucleotide, `G' is gap etc. |
| match | `-' if a match is present in this position, `!' otherwise (used in blast2col). |
| query_residue | Query sequence in searches. |
| query_seqpos | Query sequence position in searches. |
| residue | Sequence symbols. |
| seq_bp | RNA base pair relative to seqpos. |
| seqpos | Sequence position number. `.' for gaps. |
| subject_residue | Hit sequence in searches |
| subject_seqpos | Hit sequence position in searches. |
| support | Shows whether RNA structure has support. `S' is support, `N' means that different sequences have different columns as pairs to this given column. `.' means no support. |
Column usage
| Column | Programs |
|---|
| align_bp | addparen ct2col extendstem nogap shiftchk stdpair support txt2col |
| alignpos | addparen col2line col2psalign col2txtalign colorpos extendstem greppos line2col nogap shiftchk stdpair support txt2col |
| color2_b | col2psalign colorpos extendstem stdpair unknown |
| color2_g | col2psalign colorpos extendstem stdpair unknown |
| color2_r | col2psalign colorpos extendstem stdpair unknown |
| color_b | col2psalign colorpos extendstem shiftchk stdpair unknown |
| color_g | col2psalign colorpos extendstem shiftchk stdpair unknown |
| color_r | col2psalign colorpos extendstem shiftchk stdpair unknown |
| intron/exon | gb2col |
| label | addparen ct2col gb2col nogap support txt2col |
| match | blast2col |
| query_residue | blast2col |
| query_seqpos | blast2col |
| residue | addparen col2fasta col2line col2psalign col2txt col2txtalign ct2col extendstem gb2col line2col shiftchk stdpair support txt2col unknown |
| seq_bp | addparen al2seqbp extendstem nogap shiftchk stdpair support |
| seqpos | addparen col2line col2psalign col2txtalign colorpos ct2col extendstem gb2col greppos line2col nogap shiftchk stdpair support txt2col |
| subject_residue | blast2col |
| subject_seqpos | blast2col |
| support | extendstem support |
Column usage
| Program | Columns |
|---|
| addparen | align_bp alignpos label residue seq_bp seqpos |
| al2seqbp | align_bp alignpos label residue seqpos |
| blast2col | match query_residue query_seqpos subject_residue subject_seqpos |
| col2fasta | residue |
| col2line | alignpos residue seqpos |
| col2psalign | alignpos color2_b color2_g color2_r color_b color_g color_r residue seqpos |
| col2txtalign | alignpos residue seqpos |
| col2txt | residue |
| colorpos | alignpos color2_b color2_g color2_r color_b color_g color_r seqpos |
| ct2col | align_bp label residue seqpos |
| extendstem | align_bp alignpos color2_b color2_g color2_r color_b color_g color_r residue seq_bp seqpos support |
| gb2col | intron/exon label residue seqpos |
| greppos | alignpos seqpos |
| line2col | alignpos residue seqpos |
| nogap | align_bp alignpos label seq_bp seqpos |
| shiftchk | align_bp alignpos color_b color_g color_r residue seq_bp seqpos |
| stdpair | align_bp alignpos color2_b color2_g color2_r color_b color_g color_r residue seq_bp seqpos |
| support | align_bp alignpos label residue seq_bp seqpos support |
| txt2col | align_bp alignpos label residue seqpos |
| unknown | color2_b color2_g color2_r color_b color_g color_r residue |
Comments, questions, etc., email
gorodkin@rth.dk.
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Last updated March 26th, 2007 by Jan Gorodkin
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