Bioinformatics Facility 

The bioinformatics facility at NCCS provides access to high-performance compute resources and programming expertise. The compute infrastructure serves scientists at NCCS to master the informatics needs of their research in a proficient and cost-effective manner.  

  • Databases
  •  Docking Tools
  • List of PPI Servers
  • Network Analysis Tools
  • Signaling and Metabolic Databases
  • System  Biology Tools






  Uniprot Protein knowledgebase database  consists of two sections:

(A) Swiss-Prot: manually annotated and reviewed.

(B) TrEMBL: automatically annotated and is not reviewed.

Includes complete and reference proteome sets.

  UniRef Sequence clusters, used to speed up sequence similarity searches.
  UniParc Sequence archive, used to keep track of sequences and their identifiers.
  NCBI Protein database collects sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
  PRINTS A collection of protein fingerprints (conserved motifs used to characterise a protein family)
  PIR Protein Information Resource (PIR), an integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies
  Pfam The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)
  Genebank Text and similarity searching of the GenBank sequence database provided by the National Center for Biotechnology Information (NCBI).
  Genedb GeneDB is a genome database for eukaryotic and prokaryotic pathogens
  NCBI Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
1. RCSB  (The Research Collaboratory for Structural Bioinformatics) The Protein Data Bank is a repository for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids.
2. CSD ( Cambridge Structural Database) The repository of small molecule crystal structures
3. ICSD ( Inorganic Crystal Structure Database) ICSD is a database of inorganic crystal structure data, contains information on inorganic crystal structures published since 1913, including pure elements, minerals, metals, and intermetallic compounds (with atomic coordinates).


(Beta-Turn Prediction Server) BTPRED predicts the location and type of beta-turns in protein sequences. Predictions are made using a combination of artificial neural networks and simple filtering rules.
5. CATH / Gene3D CATH classifies protein structures (downloaded from the Protein Data Bank) and domains into superfamilies’ when there is sufficient evidence that they have diverged from a common ancestor.
6. Swiss model repository It is a repository for protein structure homology models
  Phylogenetic  analysis    
1. PHYLIP ( PHYLogeny Inference Package) PHYLIP is a free package of programs for inferring phylogenies.
2. web server is dedicated to reconstructing and analyzing phylogenetic relationships between molecular sequences.
3. moyble@pasteur Create workflows and save them for fast and easy reuse
(A) Global alignment    
2. Clustal omega Clustal Omega is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments.
3. Clustal w2 ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.
4. Expasy  
5. MAFT Multiple alignment program for amino acid or nucleotide sequences
(B) Local alignment    
1. blastp


Search protein database using a protein query


Algorithms used: blastp, psi-blast, phi-blast, delta-blast
2. blastn &LINK_LOC Search a nucleotide database using a nucleotide query


Algorithms used: blastn, megablast, discontiguous megablast
3. blastx BlastSearch&LINK_LOC Search protein database using a translated nucleotide query
4. tblastn &LAST_PAGE Search translated nucleotide database using a protein query
5. tbblastx &LAST_PAGE Search translated nucleotide database using a translated nucleotide query


GPU Computing  HP Proliant SL6500        SGI Altix XE 1300 Cluster

2x Intel Xeon X5675 @3.06GHz/6 core/12MB L3 Cache
96 GB (8 GB x 12) PC3 – 10600 (DDR3 – 1333) Registered DIMM memory
2 x 1 TB hot Plug SATA Hard Disk @7200 rpm
Integrated Graphics ATI RN50/ES1000 with 64 MB memory
2x NIVIDIA Tesla 2090 6 GB GPU computing module

iMAC: For running specialized software like Biojade          APC UPS 10 KVA for supporting the HPCF


Dr. Shailza Singh, Scientist E, In-charge, Bio-Informatics





Phone: 020-25708295/8296

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