Biointelligence

October 28, 2009

Useful Bioinformatics Links

Here are some useful and handy bioinformatics links which would aid in study of bioinformatics and various related fields:

http://www.cellbiol.com/

http://www.expasy.org/links.html

http://www.biochemweb.org/databases.shtml

http://bioinformatics.byu.edu/

http://www-personal.umich.edu/~lpt/chemlinks.htm

http://www.sciencegateway.org/tools/index.html

http://molbiol-tools.ca/

http://dorakmt.tripod.com/mtd/biomed.html

http://www.bio.ku.dk/mundy/links.htm

http://users.breathe.com/hachen/mol_biol_sites.html

http://www.whitney.ufl.edu/resources/molecular-links.htm

http://bioinformatics.ws/index.php/Bioinformatics_tools_and_algorithms

http://fruitfly4.aecom.yu.edu/molbio.html

http://www.biologie.uni-erlangen.de/mpp/pages/tools_prot.html

http://staff.umt.edu.my/~cha_ts/Cha%20Bioinfo.html

October 22, 2009

The Structural Genomics Knowledgebase

Filed under: Bioinformatics,Computational Biology,Proteomics — Biointelligence: Education,Training & Consultancy Services @ 5:05 am
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Biology has become an increasingly data-rich subject. Many of the emerging fields of large-scale data-rich biology are designated by adding the suffix ‘-omics’ onto previously used terms. The importance to the life-science community as a whole of such large-scale approaches is reflected in the huge number of citations to many of the key papers in these fields; the human and mouse genome papers being the most obvious examples.

Well, in true sense, “Omics” is a general term for a broad discipline of science and engineering for analyzing the interactions of biological information objects in various ‘omes’. The main focus is on:
1) mapping information objects such as genes, proteins, and ligand.
2) finding interaction relationships among the objects
3) engineering the networks and objects to understand and manipulate the regulatory mechanisms
4) integrating various omes and omics subfields.

Structural Genomics is one such stream where a proper study of cellular and genetic components is performed. The RCSB Protein Data Bank (PDB) offers online tools, summary reports and target information related to the worldwide structural genomics initiatives from its portal at http://sg.pdb.org.

There are currently three components to this site:
1) Structural Genomics Initiatives contains information and links on each structural genomics site, including progress reports, target lists, target status, targets in the PDB and level of sequence redundancy.
2) Targets provides combined target information, protocols and other data associated with protein structure determination
3) Structures offers an assessment of the progress of structural genomics based on the functional coverage of the human genome by PDB structures, structural genomics targets and homology models.

This is a free, comprehensive resource produced in a collaboration between the Protein Structure Initiative (PSI) and Nature Publishing Group (NPG) and is of a great help to the scinetific research community.

More about this can be read at: http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D302

October 13, 2009

QuickGo: A browser for Gene Ontology

Filed under: Bioinformatics,Computational Biology,Systems Biology — Biointelligence: Education,Training & Consultancy Services @ 12:44 pm
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The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. The aims of the Gene Ontology project are threefold:
1. Firstly, to maintain and further develop its controlled vocabulary of gene and gene product attributes.
2. Secondly, to annotate genes and gene products, and assimilate and disseminate annotation data.
3. Thirdly, to provide tools to facilitate access to all aspects of the data provided by the Gene Ontology project.

QuickGO is a web-based tool which allows easy browsing of the
Gene Ontology and all associated GO annotations provided by the
GOA group. It provides a comprehensive set of both electronic and
manual annotations from a large number of curation groups.QuickGO users can view and search information provided for GO terms (identifiers, words/phrases in the title or definition, cross-references and synonyms), as well as protein data from Uni- ProtKB (accession numbers, names and gene symbols). Results are ranked so that terms most closely matching the query are returned first. Individual words and combinations of words are scored according to the field in which they occur and their frequency within GO.

QuickGO is updated weekly with protein names, gene symbols, accessions and taxonomy data from UniProtKB. Single or multiple protein accessions can be queried and selected proteins will display all associated GO annotations, both electronic and manual.

QuickGo can be accessed from the EBI website. Here is the link:
http://www.ebi.ac.uk/QuickGO/

October 12, 2009

MISTRAL: For Multiple Protein Structure Alignment

Filed under: Bioinformatics,Computational Biology,Proteomics — Biointelligence: Education,Training & Consultancy Services @ 9:50 am
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With a rapidly growing pool of known tertiary structures, the importance of protein structure comparison parallels that of sequence alignment. Detecting structural equivalences in two or more proteins is computationally demanding as it typically entails the exploration of the combinatorial space of all possible amino acid pairings in the parent protein.

A new tool MISTRAL has been developed for multiple protein alignment based on the minimization of an energy function over the low-dimensional space of the relative rotations and translations of the molecules.

An alignment of upto 20 sequences in PDB format can be submitted at a time, where the length of each protein sequence is limited to 500 amino acids. It can be used both a standalone version or can be accessed online. MISTRAL can be accessed online here: http://ipht.cea.fr/protein.php

October 7, 2009

BioSytems: A New Database for Biological Systems

Filed under: Bioinformatics,Systems Biology — Biointelligence: Education,Training & Consultancy Services @ 1:08 pm
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Biological Systems are basically formed when a group of molecules interact together. A type of Biological Systems is a biological pathway. Basically a biological pathway comparises of interacting genes, proteins, and small molecules.An understanding of the components, products, and biological effects of biosystems can lead to better understanding of biological processes in normal and disease states, elucidation of possible drug effects and side effects, and other insights to complex processes that have implications for health and medicine.

NCBI has designed a BioSystems database which has a centralized access to existing pathway databases.

Current source databases supported by Biosystems database are:

1. KEGG: Kyoto Encyclopedia of Genes and Genomes (http://www.genome.jp/kegg/) by the Kanehisa Laboratory of the Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan.

2. BioCyc (http://biocyc.org/) is a collection of organism-specific pathway/genome databases (PGDBs), and the EcoCyc (http://ecocyc.org/) subset of BioCyc is included in the NCBI BioSystems database.

3. Reactome (http://www.reactome.org/) is a curated knowledge base of biological pathways, and the human subset of Reactome is included in the NCBI BioSystems database. More about the Biosystems database can be read here: http://www.ncbi.nlm.nih.gov/Structure/biosystems/docs/biosystems_help.html

October 6, 2009

Dinucleotide Properties Genome Browser: DiProGB

Filed under: Bioinformatics,Computational Biology — Biointelligence: Education,Training & Consultancy Services @ 6:08 am
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Whole genomes have now been sequenced from a long time. The basic aim of computational genome analysis is to understand the information encoded in the genomes. Apart from the nucleotide sequence, the related physical properties also play an important role.

DiProGB is a standalone computer program written in VC++.It is an easy to use new genome browser that encodes the primary nucleotide sequence by thermodynamical and geometrical dinucleotide properties. The nucleotide sequence is thus converted into a sequence graph. This visualization, supported by different graph manipulation options, facilitates genome analyses, because the human brain can process visual information better than textual information. Also, DiProGB can identify genomic regions where certain physical properties are more conserved than the nucleotide sequence itself.DiProGB adds a new dimension to the common genome analysis approaches by taking into account the physical properties of DNA and RNA.

In DiProGB all annotated features such as genes, exons, introns or repeat regions and the corresponding qualifiers such as gene name, product and function can be separately addressed and specifically colored. All or parts of the annotated information can be displayed for either a single strand or for both strands together. Overlapping features are visualized by stacked bars in the so-called feature graph below the sequence graph.

More about DiProGB can be read from here:
http://diprogb.fli-leibniz.de/introduction.php