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NCBS - IWS

National Centre for Biological Sciences - Integrated Web Server (NCBS-IWS) is an integrated bioinformatics work bench dedicated for complete in-silico analysis of protein sequence and structure data based on various strategies. Currently NCBS-IWS provides tools for 10 in-silico analysis categories. NCBS-IWS provides web interface to both in-house and widely accepted programs from major bioinformatics groups also. NCBS-IWS also provides interactive images for Analysis Work Flow, that will help the user to carry out analysis in an easy way.


NCBS-IWS Help Page :
Protein Sequence Retrieval :
Seqret is a web interface to retrieve the sequence data from Swiss-Prot Databaseusing simple user queries. Users can retrieve the data using Swiss-Prot id or key words. The out put files will be a single flat file in FASTA format). The query will be highlighted in red color.
User Query Example: 39579221 or GLP1 or Homo sapiens or Kinase

Protein Sequence Search :
Protein Sequence Search module in the NCBS-IWS provides sensitive sequence search techniques to identify remote homologues using CASCADE PSI-BLAST, Searching for similar sequences using a simultaneous scan of multiple sequence motifs using SCANMOT. Protein Sequence search also provides HMMSEARCH, PSI-BLAST and PHI-BLAST Search option against the PASS2 Database to identify structural templates for a given sequence.
User Query Example : Sequence in FASTA format
Sequence Alignment :
Protein Sequence Alignment module in the NCBS-IWS provides FMALIGN (pair wise and multile alignment) and MALIGN programs for multiple alignment.
User Query Example
FMALIGN : Set of FASTA Sequences
MALIGN : Set of PIR Format files

Sequence Analysis :
Protein Sequence Analysis module in NCBS-IWS provides various tools to perform various analysis on Protein Sequence. User Query Example :
DIAL : Sequence in FASTA format MOTIFS : Set of FASTA Sequences Sequence Analysis & Secondary Structure Prediction Meta-server :Flat file format
NB: The response time of Remote Server may take few minutes to retreive the results
ALISTAT for Alignment : Alignment files in FASTA or PIR format
ALISTAT for Sequence or Set of Sequences : Set or single FASTA format files

Structure Analysis :
Protein Structure Analysis in NCBS-IWS provides various tools to perform analysis on Protein Structure.
User Query Example : For all the tools in this module, the input is PDB File
Protein Modeling & Structure Validation:
Protein Modeling and Structure Validation in NCBS-IWS provides MODELLER, MODIP and HARMONY to perform Protein Modeling, Disulphide Bond Modeling and Structure Validation
User Query Example : MODELLER : Submit an alignment file in PIRformat and the structural template file in PDB File format
Please click here for a sample alignment file and PDB File.
Detailed Help on MODIP is available here Detailed Help of HARMONY is available here
PHYLOGENY:
Phylogeny Module provides a quick and easy access to several Phylogenetic Analysis realted programs.
  • PROTPARS
    Sample Input File available here: Details about PROTPARS available here
  • PROTDIST
    Sample Input File available here: Details about PROTDIST available here
  • PROML
    Sample Input File available here: Details about PROML available here
  • PROMLK
    Sample Input File available here: Details about PROMLK available here
  • SEQBOOT
    Sample Input File available here: Details about SEQBOOT available here
  • CONSENSE
    Sample Input File available here: Details about CONSENSE available here
  • NEIGHBOR
    Sample Input File available here: Details about CONSENSE available here
  • KITSCH
    Sample Input File available here: Details about CONSENSE available here
    Contact:
    Dr. R. Sowdhamini (mini@ncbs.res.in)
    Shameer Khadar