Rhone-Alpes Bioinformatics Center



Network Protein Sequence @nalysis

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@ ?
- sequence (HELP).
- sequence base in Pearson/FASTA format (HELP).
- 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.

Use NPS@

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