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If you use this service, could you please send us a mail to npsang@ibcp.fr with details about your usage of the NPSA service (tools used, frequency, type of sequence, ..) ? Could you explain what makes this service unique for you ? Could you please add information about your country and your laboratory ? Thanks

NPS@ stands for Network Protein Sequence @nalysis.

NPS@ is an interactive Web server dedicated to protein sequence analysis and available for the biologist community at URL: https://npsa-prabi.ibcp.fr/.

NPS@ is the "protein part" of the "Pôle Bio-Informatique Lyonnais" (PBIL).

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

• Sequence similarity search with FASTA, BLAST, PSI-BLAST, and SSEARCH on protein databases such as SWISS-PROT, SP-TrEMBL or NRL_3D.
• Sites and signatures detection with PATTINPROT or PROSCAN. PATTINPROT allow a search of one or several pattern on a protein database or on an individual sequence. PROSCAN scan a protein sequence against PROSITE.
• Multiple alignment with CLUSTALW or MULTALIN.
• Secondary structure prediction with 12 differents methods and a consensus prediction of those methods. Available methods are SOPM, SOPMA, HNN, MLRC, DPM, DSC, GORI, GORII, GORIV, PHD, PREDATOR and SIMPA96.
• Primary structure analysis such as : physico-chemical profiles (7 profiles), coil-coiled detection (Lupas method), helix-turn-helix DNA-binding motifs preditcion (Dodd & Egan), amino-acids composition and sequence coloring.

What do you need to use NPS@ ?

• a sequence (HELP).
• a sequence base in Pearson/FASTA format (HELP).
• a pattern with PROSITE syntax (HELP).

What are NPS@'s strong points ?

• All methods proposed by NPS@ are piped.
  The ouput of one method could be the input of another one. For example, after you've performed a BLAST search, you can make a database of full or partial sequences. Thenafter, this database could be aligned by multiple alignment programs (CLUSTALW,MULTALIN), filtered by a pattern search (PATTINPROT) or you can apply NPS@'s methods on each sequence of the database. And this, with no cut and paste.
• You can insert secondary structure prediction in multiple alignment.
• You can upload your own database and apply NPS@'s methods on it.
• You can download NPS@'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 (NRL-3D), you have some useful links to retrieve and work with 3D data.
• NPS@ offers links on international databases (SWISSPROT, PROSITE, CATH, SCOP,...).
• NPS@ works with data of an ACNUC query.

NPS@'s help index.

NPS@'s news.

On the CPU time allowed on NPS@
The CPU time can't be above 3 hours for a job. For bigger job, you can contact us.

NPS@'s flow chart

NPS@'s story
April 9th, 1998 : NPS@ version 1 is available. This first version was written by G.DELEAGE, C.COMBET, C.GEOURJON and C.BLANCHET.
April 2th, 1999 : NPS@ version 2 is available. This second version was written by C.COMBET, C.GEOURJON, C.BLANCHET and G.DELEAGE.
NPS@ is the "little web brother" of ANTHEPROT and MPSA softwares. The guiding philosophy is the same for these two softwares and for this "webware".
We hope they are useful and easy-to-use...

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 developping this server.

Who are we

NPS@'s supports

• MESR (ACC-SV13)
• CNRS (IMABIO, COMI, GENOME)
• Région Rhône-Alpes (Programme EMERGENCE)

Statistics and number of jobs performed