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 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@More on http://npsa-pbil.ibcp.fr ...