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Bioinformatics Tools - Databases, Alignment, Evolutionary and Protein Analysis
#5
Here are some new and freely accessible biomedical databases:

Drug2Gene: It’s free and unifies a number of popular public resources to provide structured and organized information for identified and reported relations between genes/proteins and drugs/compounds. It allows user’s interactive management by the ability to flag, comment and update relations, to import new drug-gene relations valuable for a specific project. Gene orthology and similarity information is matched to certain relationship entries assisting the prediction of new unreported drug-gene associations. You can go to the original source of the reported relation and explore for more facts, details and evidences...
PhenomicDB: It's a free multi-organism phenotype-genotype data repository unifying a variety of primary sources to make phenotypic data from a wide range of species and model organisms simultaneously searchable, visible and comparable. Gene orthology and similarity information mapped to particular entries, and the phenotypic data clustering system, provide facilities for the discovery of new phenotypic manifestations of a given genotype. Reported genotype-phenotype relationships are supported by evidence and reference links.
Here is a free online tool for text extraction analysis (new functionalities are to be added):

WebRT: Metalife Web Recognition Tool is a light text mining tool developed for online text analysis of diverse-type biomedical and molecular biology literature contents. Its main function is terms/phrase extraction and categorization with the ability to recognize synonyms, acronyms and spelling variations, to normalize and unify hits, to distinguish between seemingly equal terms with different categorization, etc. Relations extraction is expected soon...
#6
Building on the recognition of the importance of information transmission, accumulation and processing in biological systems, in 1978 Paulien Hogeweg, coined the term "Bioinformatics" to refer to the study of information processes in biotic systems.[1] This definition placed bioinformatics as field parallel to biophysics and biochemistry. Examples of relevant biological information processes studied in the early days of bioinformatics are the formation of complex social interaction structures by simple behavioral rules, and the information accumulation and maintenance in models of prebiotic evolution.

At the beginning of the "genomic revolution", the term bioinformatics was re-discovered to refer to the creation and maintenance of a database to store biological information such as nucleotide sequences and amino acid sequences. Development of this type of database involved not only design issues but the development of complex interfaces whereby researchers could access existing data as well as submit new or revised data.
#7
(10-04-2012, 04:47 PM)Thomast22 Wrote: Building on the recognition of the importance of information transmission, accumulation and processing in biological systems, in 1978 Paulien Hogeweg, coined the term "Bioinformatics" to refer to the study of information processes in biotic systems.[1] This definition placed bioinformatics as field parallel to biophysics and biochemistry. Examples of relevant biological information processes studied in the early days of bioinformatics are the formation of complex social interaction structures by simple behavioral rules, and the information accumulation and maintenance in models of prebiotic evolution.

At the beginning of the "genomic revolution", the term bioinformatics was re-discovered to refer to the creation and maintenance of a database to store biological information such as nucleotide sequences and amino acid sequences. Development of this type of database involved not only design issues but the development of complex interfaces whereby researchers could access existing data as well as submit new or revised data.

We all know that biological research is a field which is an ongoing process. This has resulted in collection of huge information on biology subject and its developments. Now this data needs to be shared to prepare the knowledge bank which can serve as a tool for future progress. Bioinformatics is playing a good role in this. Data collection, its correlation, analysis and finding the application are mainly possible due to bioinformatics. New improvements in data collection are ongoing process and the challenge is to provide a way to store the data such that it is user-friendly with ability of compatibility with new upcoming ways of data storage. Much new software is now a day’s available for finding the data for specific genome or proteins like Nucleic Acids research database, proteomics database, metabolomics database, gene expression ways, Gene location in genome etc.
Today’s software in bioinformatics are not only user friendly but also have lot of database within the system which provide all option to create own user-friendly interface while working, like workflow systems, which provides user option of sharing the workflow and providing the results online. Galaxy, Taverna is the best examples of it. With the help of Bioinformatics data up to the level of prediction of gene sequence is possible, protein 3-Dimensional modeling with animation are being done in research fields, Also comparison of any cellular morphology with the other tissues of same or other species is easily done. One of the most uses of this database is being one protein engineering technique which provides all information at the time of research which reduces the time and is cost efficient.
#8
Bioinformatics is the science concerned with the development and application of computer hardware and software to the acquisition, storage, analysis and visualization of biological information.

A database is a vast collection of data pertaining to a specific topic, e.g., nucleotide sequence, protein sequence etc., in an electronic environment. Databases are the heart of bioinformatics. There are a very large number of databases, which is growing rapidly.
The utilization of various databases requires the use of suitable search engines and analysis tools. These tools are often called database mining tools and the process of database utilization is known as database mining.

BLAST (Basic Local Alignment Search Tool) is a family of user-friendly sequence similarity search tools on the web. The BLASt server is supported through NCBI, USA. This tool is designed to identify potential homologues for a given sequence. It can analyze both DNA and protein sequences. Identification of homologues allows the prediction of potential functions and in modeling of the 3-D structure. A local alignment finds the optimal alignment between sub regions or local regions of the specified sequences. A local alignment search tool is used to find sequence motifs, domains, etc.

There are several BLAST programmes. Each of them serves as specific purpose. The different types of BLAST programmes are briefly described below. The new BLAST programmes are called BLAST 2.0.

1. BLASTp. It compares the submitted protein sequence against a protein database.
2. BLASTx. This programmes translates the submitted nucleotide sequence into amino acid sequence and compares the latter with a protein database.
3. BLASTn. This is used to compare a nucleotide sequence with a nucleotide sequence database.
4. tBLASTn. The programme converts the submitted protein sequence into nucleotide sequence and compares it with nucleotide sequence database.
5. tBLASTx. This programme translates the submitted nucleotide sequence as well as the nucleotide sequence database into amino acid sequences and searches for homology between the two.

ENTREZ.
It is one of the most popular search engines at NCBI, USA. It searches bibliographic citations and biological data from a variety of reliable databases, viz., SWISS-PROT, PDB, GeneBank, and EMBL etc. It offers a variety of criteria of information, e.g., all possible citations from a given author that deal with a given subject that deal with a given subject, standard names for given genes, a given sequence database etc.
  

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