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
|
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 |
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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 |
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iMAC: For running specialized software like Biojade APC UPS 10 KVA for supporting the HPCF |
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Dr. Shailza Singh, Scientist E, In-charge, Bio-Informatics
Email: singhs@nccs.res.in
Phone: 020-25708295/8296