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

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

Upload your own Pearson/FASTA sequence file.

Sequence homology search :

• against protein sequence databases :
  • BLAST (query protein (blastp) or nucleotide (blastx) sequence)
  • PSI-BLAST (query protein sequence)
  • FASTA (query protein sequence)
  • SSEARCH (query protein sequence)
  • HMMSEARCH (query protein profile, HMMER 3 format)
• against nucleotide sequence databases :
  • BLAST (query protein (tblastn) or nucleotide (blastn, tblastx) sequence)
  • FASTA (query nucleotide sequence)
  • SSEARCH (query nucleotide sequence)

Multiple sequence alignment :

• with protein sequences :
  • KALIGN
  • MAFFT
  • MUSCLE
• with nucleotide sequences :
  • KALIGN
  • MAFFT
  • MUSCLE

Profile HMM building :

• HMMBUILD: build a profile HMM with HMMER 3

Protein secondary structure prediction :

• using one method:
  • DSC
  • GOR IV
  • MLRC
  • PREDATOR
  • SIMPA96
  • SOPMA
• combining several methods

Miscellaneous protein primary structure analysis :

• Coiled-coil domain prediction
• Coloring of amino-acid residues
• Composition in amino-acid residues
• Helix-turn-helix (HTH) DNA-binding motif prediction
• PROSITE motifs / patterns / signatures scan (PROSCAN) for protein domains, families and functional sites annotation

Geno3D : comparative modelling of protein 3-D structure.

References about databases and software integrated into NPS@.

Acknowledgments :

• All Bioinformatics teams for their database and software developments
• ENA, Ensembl, EnsemblGenomes, UniProtKB, PDB, MGnify and AlphaFoldDB databases are updated from European Bioinformatics Insitute (EBI)
• PROSITE database is updated from Expasy portal of Swiss Institute of Bioinformatics (SIB)
• ESM Metagenomic Atlas from the original server

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