Help with the result files and zip archives
In some instances errors can occur with a job because of illegal characters appearing in the email address, the sequence data, or even the sequence title.
Results in PDF format
This server publishes results in PDF format. PDF is the Portable Digital Format created by Adobe to facilitate easy transfer of complex documents for viewing and printing at high quality. To view a PDF file you need the Adobe Acrobat Reader or the Acrobat Plug-in for your browser. These can be obtained from the Adobe web site below.
Get Acrobat Reader - Adobe Web Site
Working with ZIP files
Windows users should be familiar with "WinZip", or at the very least "pkunzip". Either of these packages will allow you to extract the collection of files from the ZIP archives that are created by this server.
Macintosh users can also work with ZIP files in a number of ways. There is an Expander Enhancement for users of Stuffit Expander which adds the ZIP archive extraction ability to your stuffit engine. Then there's the dedicated ZipIt! package which lets you create and extract ZIP files.
Macintosh: ZipIt! version 1.3.5
The contents of the results archive
This section will describe the contents of each file contained in the mfold archive that is generated from each mfold submission.
Energy Dot Plot (plot.pdf, plot.txt)
The energy dot plot displays the superposition of all possible foldings within a user specified energy increment from the computed minimum. In this triangular plot, a dot in row i and column j represents a base pair between ribonucleotides i and j. Different colors are used to represent the different levels of suboptimality. The energy dot plot is given as a text file (plot.txt) and the diagram as a pdf file (plot.pdf).
Secondary Structures (mseq_x.pdf,mseq_x.ct)
A diagramatic view of the secondary structures are created as pdf files. The corresponding .ct files are also provided.
Output Files (mseq.out, mseq.ct, mseq.reg)
The .out file gives you a rough but direct interpretation of the sequence folding, while the .ct file is intended to be used as an input to other software which draws secondary structures or to analyse a large number of suboptimal foldings. The .reg file can also be used in this way, but is more condensed than the .ct file and lacks sequence information.
Sequence Print Out (mseq_.pnt)
A simple printout of the submitted sequence is included with each ten nucleic acids numbered.