logo
logo

Column descriptions
Column Description
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@genome.ku.dk.


Last updated March 26th, 2007 by Jan Gorodkin