Services

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

Databases

Sno

Database

Site

Use

  Protein    
  Uniprot http://www.uniprot.org/ 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 http://www.uniprot.org/uniref/ Sequence clusters, used to speed up sequence similarity searches.
  UniParc http://www.uniprot.org/uniparc/ Sequence archive, used to keep track of sequences and their identifiers.
  NCBI http://www.ncbi.nlm.nih.gov/protein/ 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 http://bioinf.man.ac.uk/dbbrowser/PRINTS/index.php A collection of protein fingerprints (conserved motifs used to characterise a protein family)
  PIR http://pir.georgetown.edu/ Protein Information Resource (PIR), an integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies
  Pfam http://pfam.xfam.org/ The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)
  Genes    
  Genebank http://www.ncbi.nlm.nih.gov/genbank/ Text and similarity searching of the GenBank sequence database provided by the National Center for Biotechnology Information (NCBI).
  Genedb http://www.genedb.org/Homepage GeneDB is a genome database for eukaryotic and prokaryotic pathogens
  NCBI http://www.ncbi.nlm.nih.gov/gene 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.
  Structure    
1. RCSB  (The Research Collaboratory for Structural Bioinformatics) http://www.rcsb.org/pdb/home/home.do 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) http://www.ccdc.cam.ac.uk/pages/Home.aspx The repository of small molecule crystal structures
3. ICSD ( Inorganic Crystal Structure Database) http://icsd.ill.eu/icsd/index.php 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).
4. BTPRED

 

(Beta-Turn Prediction Server)
http://www.biochem.ucl.ac.uk/bsm/btpred/index.html 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 http://www.cathdb.info/ 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 http://swissmodel.expasy.org/repository/ It is a repository for protein structure homology models
  Phylogenetic  analysis    
1. PHYLIP ( PHYLogeny Inference Package) http://bioweb2.pasteur.fr/ PHYLIP is a free package of programs for inferring phylogenies.
2. Phylogeny.fr http://www.phylogeny.fr/ Phylogeny.fr web server is dedicated to reconstructing and analyzing phylogenetic relationships between molecular sequences.
3. moyble@pasteur http://mobyle.pasteur.fr/cgi-bin/portal.py#welcome Create workflows and save them for fast and easy reuse
  Alignment    
(A) Global alignment    
1. CLUSTALw http://www.genome.jp/tools/clustalw/  
2. Clustal omega http://www.ebi.ac.uk/Tools/msa/clustalo/ 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 http://www.ebi.ac.uk/Tools/msa/clustalw2/ ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.
4. Expasy http://www.ch.embnet.org/software/ClustalW.html  
5. MAFT http://www.ebi.ac.uk/Tools/msa/mafft/ Multiple alignment program for amino acid or nucleotide sequences
(B) Local alignment    
1. blastp http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM&PAGE_TYPE

BlastSearch&LINK_LOC

Search protein database using a protein query

 

Algorithms used: blastp, psi-blast, phi-blast, delta-blast
2. blastn http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM&PAGE_TYPE &LINK_LOC Search a nucleotide database using a nucleotide query

 

Algorithms used: blastn, megablast, discontiguous megablast
3. blastx http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM&PAGE_TYPE BlastSearch&LINK_LOC Search protein database using a translated nucleotide query
4. tblastn http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM&PAGE_TYPE&BLAST_SPEC=&LINK_LOC &LAST_PAGE Search translated nucleotide database using a protein query
5. tbblastx http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM&PAGE_TYPE&BLAST_SPEC=&LINK_LOC &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

 

Email: singhs@nccs.res.in

 

 


Phone: 020-25708295/8296

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