This site is a fork of the original PRABI NPS@ server

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July 30, 2024: NPS@ updated (see NEWS).

NPS@ stands for Network Protein Sequence Analysis (NPSA altered in NPS@ to refer to its access by the Internet network).

NPS@ is an interactive Web server dedicated to protein sequence analysis available for the biologist community.

NPS@ is the little web "brother" of ANTHEPROT and MPSA software. The guiding philosophy is the same for these two software and for this "webware". We hope they are useful and user-friendly.

NPS@ is one service of the "Pôle Rhône-Alpes de Bio-Informatique" (PRABI).

NPS@'s history

• December 18th, 2019 : this NPS@ fork opening at https://npsa.lyon.inserm.fr by Christophe Combet.
• February 17th, 2003 : NPS@ version 3 is available. This third version was written by Christophe Combet, Céline Charavay, Christophe Geourjon, Christophe Blanchet and Gilbert Deléage.
• April 2nd, 1999 : NPS@ version 2 is available. This second version was written by Christophe Combet, Christophe Geourjon, Christophe Blanchet and Gilbert Deléage.
• April 9th, 1998 : NPS@ version 1 is available. This first version was written by Gilbert Deléage, Christophe Blanchet, Christophe Combet and Christophe Geourjon.

What kind of analysis can you carry out with NPS@ ?

• Homology search by means of pairwise sequence alignment or position-specific scoring matrix / profile: FASTA, BLAST, PSI-BLAST and SSEARCH on sequence databases such as European Nucleotide Archive (ENA), UniProt Knowledge Base (UniProtrKB, Swiss-Prot), Protein Data Bank (PDB), AlphaFold Database or ESM Metagenomic Atlas .
• Multiple sequence alignment with KALIGN, MAFFT, MUSCLE .
• Protein secondary structure prediction including a consensus prediction of those methods. Available methods are DSC, GORIV, MLRC, PREDATOR, SIMPA96, SOPMA .
• Primary structure analysis such as : Coil-coiled domains prediction, Coloring of amino-acid residues, Composition in amino-acid residue, Helix-Turn-Helix (HTH) DNA-binding motif prediction and PROSITE motifs / patterns / signatures scan (PROSCAN) for protein domains, families and functional sites annotation .

What do you need to use NPS@ ?

• one sequence (see help).
• a sequence file in Pearson/FASTA format (see help).

What are NPS@'s strong points ?

• All methods proposed by NPS@ are piped. The output of one method could be the input of another one. For example, after you've performed a sequence similarity search (e.g. BLAST), you can make a database of full or partial sequences. Thereafter, these sequences could be aligned by multiple sequence alignment programs (e.g. KALIGN, MAFFT, MUSCLE), or you can apply NPS@'s methods on each sequence of the database. And this, with no cut and paste, as data transfer are done on server side and format conversion are ensured when needed.
• You can insert protein secondary structure prediction in multiple sequence alignment.
• You can upload your own sequence file and apply NPS@'s methods on it.
• You can download NPSA's data in protein sequence analysis softwares on your local computer for further analysis, to save them or insert them in an article.
• The NPSA link allows you to apply NPS@'s methods on a sequence. Even more, when the sequence comes from a 3D database (PDB), you have some useful links to retrieve and work with 3D data.
• NPS@ offers links on international databases (e.g. ENA, UniProtKB, Swiss-Prot, PDB).

NPS@'s flow chart.

NPS@'s help index page.

To cite NPS@:
NPS@: Network Protein Sequence Analysis
TIBS 2000 March Vol. 25, No 3 [291]:147-150
Combet C., Blanchet C., Geourjon C. and Deléage G.

We will be glad to receive a reprint of article citing NPS@.
This will be a contribution and an encouragement in developing this server.

NPS@'s limitations:
The CPU time can't exceed 30 minutes for one computation. For longer job, you can contact us.

View number of jobs performed by NPS@.

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