Mirror sites

Sl. no
Short description
Major Bioinformatics Resources/ Databases
1. NCBI - National Centre for Biotechnology Information
Most popular composite database with number of genomics, proteomics tools, Databases, literature database.
2. EBI - Europian Bioinformatics Institute
One of the major bioinformatics resource as that of NCBI having tools, Databases for genomics, proteomics tools etc.
3. ExPASy - Expert Proteomics Server
The server is a collection of tools for protein analysis. There tools present were arranged in the order from primary sequence analysis to tertiary structure prediction.
4. EMBL - The European Molecular Biology Laboratory
The European Molecular Biology Laboratory (EMBL) is a molecular biology research institution supported by 20 European countries and Australia as associate member state. The cornerstones of EMBL's mission are: to perform basic research in molecular biology and molecular medicine, to train scientists, students and visitors at all levels, to offer vital services to scientists in the member states, to develop new instruments and methods in the life sciences, and to actively engage in technology transfer.
5. TIGR - The Institute of Genomic Research
TIGR is an resource for software, mathematical tools, and databases to assemble and analyze these genomes .
6. Wellcome Trust Sanger Institute
The Wellcome Trust Sanger Institute (formerly the Sanger Centre) is a genome research centre in the Wellcome Trust Genome Campus in Cambridgeshire, England .
7. NHGRI - National Human Genome Research Institute
The National Human Genome Research Institute (NHGRI) is a division of the National Institutes of Health, located in Bethesda, Maryland. NHGRI began as the National Center for Human Genome Research (NCHGR), which was established in 1989 to carry out the role of the NIH in the International Human Genome Project (HGP) .
8. DDBJ - DNA Data Bank of Japan
The DNA Data Bank of Japan is a DNA data bank. It is located at the National Institute of Genetics of Japan. It is also a member of the International Nucleotide Sequence Database Collaboration or INSDC. It shares its data with European Molecular Biology Laboratory at the European Bioinformatics Institute and with GenBank at the National Center for Biotechnology Information.
9. Swissprot - Swiss Institute of Bioinformatics
The most curated protein database available till date .
10. PIR -Protein Information Resource The largest protein sequence Database.
11. PDB - Protein Data Bank
Archive of experimentally-determined, biological macromolecule 3-D structures from the Brookhaven National Laboratory .
12. KEGG - Kyoto Encyclopedia of Genes and Genomes
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of online databases dealing with genomes, enzymatic pathways, and biological chemicals. The PATHWAY database records networks of molecular interactions in the cells, and variants of them specific to particular organisms .
13. PFAM - Protein Family Database
Pfam is a large collection of multiple sequence alignment and hidden Markov models covering many common protein domains and families. For each family in Pfam you can: Look at multiple alignments, View protein, domain architectures, Examine species distribution, Follow links to other databases and View known protein structures .
PROSITE is a database of protein families and domains. It consists of entries describing the domains, families and functional sites as well as amino acid patterns, signatures, and profiles in them .
15. CATH - Class Architecture Topology Homologous superfamily CATH defines four classes: mostly-alpha, mostly-beta, alpha and beta, few secondary structures.
16. SCOP - Structural Classification of Proteins
The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification
17. PDBSum
PDBsum provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them.
18. LigandInfo
Ligand.Info is a compilation of various publicly available databases of small molecules such as ChemBank, ChemPDB, KEGG, NCI, AKos GmbH, Asinex Ltd, and TimTec. The total size of the Meta-Database is 1 million entries. The compound records contain calculated three-dimensional coordinates and sometimes information about biological activity. Some molecules have information about FDA drug approving status or about anti-HIV activity. Meta-Database can be downloaded in SDF format and used for virtual high-throughput screening of new potential drugs. The database can also be screened using a Java-based tool.

Major Bioinformatics tools/ WorkBench/ Software resources
19. BLAST - Basic Local Alignment Search Tool
BLAST 2.0, (Basic Local Alignment Search Tool), provides a method for rapid searching of nucleotide and protein databases.
20. FASTA - FAST Alignment
The FastA program has been developed by Pearson & Lipman (1988) and is useful to find all protein sequences of a database such as Swiss-Prot, that are homologous to a given sequence.
21. ClustalW
Clustal-W is a multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analyzing the results.
22. ClustalX
ClustalX is a new windows interface for the ClustalW. It provides an integrated environment for performing multiple sequence and profile alignments and analyzing the results .
EMBOSS, The European Molecular Biology Open Source Software Suite, is a package of high-quality FREE Open Source software for sequence analysis .
24. Biology WorkBench
A profile hidden Markov model that can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus .
26. MEGA
MEGA is an integrated tool for automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses .
27. MFold
Mfold is an RNA and DNA folding package.
PHYLIP is a free package of programs for inferring phylogenies .
29. MUMmer
MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.
30. PrimerDesign
Primer Design is a DOS-program to choose primer for PCR or oligonucleotide probes. It is tailored to check known sequences for repeats and unique sequences and subsequently to create prober primers according to this data. A lot of constrains are available to meet your conditions. It can handle up to 32000 base pairs.
31. Sequin
Sequin is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank, EMBL, or DDBJ sequence databases. It is capable of handling simple submissions that contain a single short mRNA sequence, and complex submissions containing long sequences, multiple annotations, segmented sets of DNA, or phylogenetic and population studies .
32. Cellware
Cellware has been designed to conduct modeling and simulation of gene regulatory and metabolic pathways and also offer an integrated environment for diverse mathematical representations, parameter estimation and optimization. In addition, a user-friendly graphical display and capability to run large and complex models would be provided by default. A very special feature of Cellware is that it would be the first grid based modeling and simulation tool in the field of Systems Biology.
33. CytoScape
Cytoscape is a visualization platform for use with molecular interaction networks. Interaction data can be integrated with other state data such as gene expression profiles. The input to Cytoscape includes lists of interaction pairs, and tab/space delimited files containing mRNA expression profiles. The nodes of the interaction networks can be filtered by such variables as GO annotations and number of interactions.
34. E-Cell 3
E-Cell Project is an international research project aiming to model and reconstruct biological phenomena in silico, and developing necessary theoretical supports, technologies and software platforms to allow precise whole cell simulation.
35. Rasmol
Rasmol is a molecular graphics program intended for the visualization of proteins, nucleic acids and small molecules .
36. SPDBViewer
Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface .
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
38. VEGA
VEGA was originally developed to create a bridge between most of the molecular software packages only, but in the years, enhancing its features, it's evolved to a complete molecular modeling suite .
39. ArgusLab
It is an incredible molecular modeling, graphics, and drug design program.
40. 3D-Dock Suite
FTDock ( Fourier Transform Dock ) performs rigid-body docking on two biomolecules in order to predict their correct binding geometry. FTDock outputs multiple predictions that can be screened using biochemical information.
GRAMM is a program for protein docking. To predict the structure of a complex, it requires only the atomic coordinates of the two molecules (no information about the binding sites is needed). The program performs an exhaustive 6-dimensional search through the relative translations and rotations of the molecules. The molecular pairs may be: two proteins, a protein and a smaller compound, two transmembrane helices, etc. GRAMM may be used for high-resolution molecules, for inaccurate structures (where only the gross structural features are known), in cases of large conformational changes, etc .
42. HEX
Hex is an interactive protein docking and molecular superposition program. Currently, Hex understands protein and DNA structures in PDB format .
43. DOCK
Dock is a powerful drug designing software developed by UCSF.
44. AutoDock
AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
45. BioJAVA
BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It include objects for manipulating sequences, file parsers, DAS client and server suport, access to BioSQL and Ensembl databases, and powerful analysis and statistical routines including a dynamic programming toolkit.
46. BioPerl
Bioperl is a collection of perl modules that facilitate the development of perl scripts for bioinformatics applications. As such, it does not include ready to use programs in the sense that many commercial packages and free web-based interfaces do (e.g. Entrez, SRS). On the other hand, bioperl does provide reusable perl modules that facilitate writing perl scripts for sequence manipulation, accessing of databases using a range of data formats and execution and parsing of the results of various molecular biology programs including Blast, clustalw, TCoffee, genscan, ESTscan and HMMER. Consequently, bioperl enables developing scripts that can analyze large quantities of sequence data in ways that are typically difficult or impossible with web based systems .
47. BioPython
An international association of developers of freely available Python tools for computational molecular biology. biopython.org provides an online resource for modules, scripts, and web links for developers of Python based software for life science research.



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SVIMS Bioinformatics Centre, BIF, Dept. of Bioinformatics, SVIMS University,Tirupati-517507