NESPript operates as a webserver. It can be accessed with any Web browser equipped with a PDF reader.

• Supported Web browsers are:

• Adobe Acrobat Reader is recommended to view the NESPript result files in PDF format - official website.

NESPript uses a pop-up window to display the results. In certain browser configurations, an ad-blocking mechanism prevents this pop-up from appearing. In this case, NESPript will display a warning box asking the user to specifically disable this security before submitting a job.

To do this, please follow the instructions below, depending on the web browser you are using:

• Apple Safari.

• Google Chrome.

• Microsoft Edge.

• Mozilla Firefox.

• Opera.

In all cases, you must allow the domain nespript.ibcp.fr
Once this is done, please restart your Web browser and submit a new job to NESPript.

For help interpreting the information in the figures produced by NESpript, please refer to this page.

The starting point for a NESPript figure is a nucleic acids multiple sequence alignment file in Clustal, FASTA or MultAlin. For example, you can obtain such an alignment using online servers such as EMBL-EBI Clustal Omega. You will then need to upload this file into NESPript to generate a simple multiple alignment figure.

If a 3D structure corresponding to a sequence is known (in PDB, CIF or DSSR format only), you can add it to the figure. Please take due note that NESPript is not able to predict nucleic acids secondary structures : it only uses experimentally determined structures or 3D models (e.g. from AlphaFold, RoseTTAFold, etc.). Finally, as there is no way to have PDB, CIF or DSSR files containing multiple structures, you must add one structure file per sequence.

You can follow the NESPript tutorials to get familiar with such process.

The Secondary structure depiction section refers to the secondary structure elements to be displayed at the top of the sequence block. By default, NESPript assumes that the secondary structure file corresponds to the first sequence in the alignment. This is not the case for you.

There are three ways to solve this problem:

• Change the sequence order in your alignment file: place the sequence line corresponding to the secondary structure file first.

or

• Change the order of the sequences in the Defining groups section of the NESPript form. Example: 10 all ⇒ means that the sequence order of your alignment will be changed so that sequence number 10 is displayed first, followed by all the others.

or

• Switch to ADV mode. In the "Special commands and characters" section of the form, enter the following command: X D 10 (and replace 10 by the line number of the alignment corresponding to the sequence for which you wish to display the secondary structure elements).

If the error message persists, check that the sequence of the alignment is identical to that of the structure file.

Note that you can insert secondary structure elements at the bottom of an alignment. To do this, switch to ADV mode.
A BOTTOM secondary structures section will now appear on the form, where you can enter a structure file as input. The latter must correspond to the last sequence of your alignment.

PDF and PostScript files generated by NESPript can be edited in programs such as Adobe Illustrator or Inkscape.
You can also generate PNG or TIFF files and use the image editing software of your choice.

Due to software licence restrictions, NESPript can only be run online from this website.

Do not hesitate to contact us (espript@ibcp.fr) if you need any further information or if you need some help with NESPript.