Help for Cofolga2mo web server

*Submission page
Retrieve results sorted by : please select the measure by which the alignments are sorted. Maximum number of outputted alignments: this value is reffered to as n_out in the IPSJ paper. Top n_out alignments in the sorted alignments is outputted as a result. Initial random number: user can change the initial random number of the genetic algorithm in Cofolga2mo.

Retrieve results sorted by : please select the measure by which the alignments are sorted.

Maximum number of outputted alignments: this value is reffered to as n_out in the IPSJ paper. Top n_out alignments in the sorted alignments is outputted as a result.

Initial random number: user can change the initial random number of the genetic algorithm in Cofolga2mo.

*Web page for sorted alignemnt list
<< Sequence info. table >> PID: the percent sequence identity of the alignment with the highest s in the obtained approximate set. In this web server, the PID after removing gapped columns is used. It is noted that the displayed PID is a very rough estimate of the true PID and is only for calculating the I. length (nt): sequence length in nucleotides. G+C content:a guanine and cytocine content for each seuqnece in percent. << GA info. table >> ini. rand. num.: initial random number for genetic algorithm. << Alignment list table >> Fold: by cricking the 'Alifold' button, the next web page opens and user can browse the predicted consensus secondary structure. I : linear weight index for selecting accurate alignments from weak Pareto optimal alignments computed by Cofolga2mo. P : structure score used in Cofolga2mo. s : sequence similarity score with affine gap penalties.

*Web page for sorted alignemnt list

<< Sequence info. table >>

PID: the percent sequence identity of the alignment with the highest s in the obtained approximate set. In this web server, the PID after removing gapped columns is used. It is noted that the displayed PID is a very rough estimate of the true PID and is only for calculating the I.

length (nt): sequence length in nucleotides.

G+C content:a guanine and cytocine content for each seuqnece in percent.

<< GA info. table >>

ini. rand. num.: initial random number for genetic algorithm.

<< Alignment list table >>

Fold: by cricking the 'Alifold' button, the next web page opens and user can browse the predicted consensus secondary structure.

I : linear weight index for selecting accurate alignments from weak Pareto optimal alignments computed by Cofolga2mo.

P : structure score used in Cofolga2mo.

s : sequence similarity score with affine gap penalties.

*Web page for predicted consensus secondary structure
<< Alignment info. table >> I : linear weight index for selecting accurate alignments from weak Pareto optimal alignments computed by Cofolga2mo. P : structure score used in Cofolga2mo. s : sequence similarity score with affine gap penalties. << VARNA usage >> ZOOM: By rotating the mouse wheel on each VARNA window, user can zoom the structure. SHIFT: User can drag and shift the structure by cricking the mouse wheel on each VARNA window. If this function does not work well, please try after ZOOMING the structure. SAVE and EXPORT: by cricking the left mouse button on the VARNA window, the following menu is displayed. Then user can select 'Save as' to save the structure in a text-based format such as CT (connectivity table format). If user selcet 'Export', user can save the structure in SVG, EPS, PNG, and JPEG. ROTAION: By selecting 'View' and then 'Rotation' in the menu, user can rotate the structure.

*Web page for predicted consensus secondary structure

<< Alignment info. table >>

I : linear weight index for selecting accurate alignments from weak Pareto optimal alignments computed by Cofolga2mo.

P : structure score used in Cofolga2mo.

s : sequence similarity score with affine gap penalties.

<< VARNA usage >>

ZOOM: By rotating the mouse wheel on each VARNA window, user can zoom the structure.

SHIFT: User can drag and shift the structure by cricking the mouse wheel on each VARNA window. If this function does not work well,

please try after ZOOMING the structure.

SAVE and EXPORT: by cricking the left mouse button on the VARNA window, the following menu is displayed.

Then user can select 'Save as' to save the structure in a text-based format such as CT (connectivity table format).

If user selcet 'Export', user can save the structure in SVG, EPS, PNG, and JPEG.

ROTAION: By selecting 'View' and then 'Rotation' in the menu, user can rotate the structure.