4 Major categories of Bioinformatics Tools

These are 4 Major categories of Bioinformatics Tools used by students, Bioinformatics professionals and Computational Biologists.

There are data-mining software that retrieves data from genomic sequence databases and also visualization tools to analyze and retrieve information from proteomic databases.

These can be classified as homology and similarity tools, protein functional analysis tools, sequence analysis tools and miscellaneous tools. 

Here is a brief description of a few of these. Everyday bioinformatics is done with sequence search programs like BLAST, sequence analysis programs, like the EMBOSS and Staden packages, structure prediction programs like THREADER or PHD or molecular imaging/modelling programs like RasMol and WHATIF.

4 Major categories of Bioinformatics Tools are:

1. Homology and Similarity Tools:

- Homologous sequences are sequences that are related by divergence from a common ancestor.
- Thus the degree of similarity between two sequences can be measured while their homology is a case of being either true of false.
- This set of tools can be used to identify similarities between novel query sequences of unknown structure and function and database sequences whose structure and function have been elucidated.

2. Protein Function Analysis:

- These groups of programs allow you to compare your protein sequence to the secondary (or derived) protein databases that contain information on motifs, signatures and protein domains.
- Highly significant hits against these different pattern databases allow you to approximate the biochemical function of your query protein.

3. Structural Analysis:

- These sets of tools allow you to compare structures with the known structure databases.
- The function of a protein is more directly a consequence of its structure rather than its sequence with structural homologs tending to share functions.
- The determination of a protein's 2D/3D structure is crucial in the study of its function.

4. Sequence Analysis:

- This set of tools allows you to carry out further, more detailed analysis on your query sequence including evolutionary analysis, identification of mutations, hydropathy regions,
- CpG islands and compositional biases.
- The identification of these and other biological properties are all clues that aid the search to elucidate the specific function of your sequence.

5 principal requirements on the public data services

These are "5 principal requirements on the public data services".
public data services provides many services in health care, commerce, research etc.

5 principal requirements on the public data services are:

• Data quality -

Data quality has to be of the highest priority. However, because the data services in most cases lack access to supporting data, the quality of the data must remain the primary responsibility of the submitter.

• Supporting data - 

Database users will need to examine the primary experimental data, either in the database itself, or by following cross-references back to network-accessible laboratory databases.

• Deep annotation - 

Deep, consistent annotation comprising supporting and ancillary information should be attached to each basic data object in the database.

• Timeliness - 

the basic data should be available on an Internet-accessible server within days (or hours) of publication or submission.

• Integration - 

each data object in the database should be cross-referenced to representation of the same or related biological entities in other databases. Data services should provide capabilities for following these links from one database or data service to another.

4 reasons to use "SYNTAX function in SPSS Commands

These are 4 reasons to use "SYNTAX" in SPSS Commands.
The syntax is basically a text file where you can add comments and SPSS commands.

4 Reasons Everyone should use the syntax function in SPSS Commands are:

• It is a way of documenting and archiving everything you have done with the data material.

• It is easy to repeat parts or all of the analysis.

• Other people involved in the data material can easily understand what you have done and how you have done it.

• It saves an enormous amount of time.

Online Basic Definitions on Statistics

These are "Online Basic Definitions on Statistics". It can boost vocabulary in Bio-Statistics.
It can also enhance basic knowledge of Bio-Statisticstics.

1. What is "A Population"?

A population1 - It is any specific collection of objects of interest.

2. What is "A measurement and sample data"?

"A measurement" is a number or attribute computed for each member of a population or of a sample.

Skills of A Bioinformatician

Bioinformatics is vast field to develope "Skills of  A Bioinformatician".
A bioinformatician needs regularly gaining of knowledge of biology, biotechnology and computer at the same time. 
here, Skills of a Bioinformatician are given which clears thoughts of what skills of bioinformatics are needed by students of bioinformatics.

Skills of a Bioinformatician :

 According to the scientist working at companies such as Celera Genomics and Eli Lilly, the following "core requirements" for bioinformaticians:

1. Fairly deep background in some aspect of molecular biology. 
It can be biochemistry, molecular biology, molecular biophysics, or even molecular modeling, but without a core of knowledge of molecular biology is like, "run into brick walls too often."

2. Understanding the central dogma of molecular biology, how and why DNA sequence is transcribed into RNA and translated into protein is vital.

3. Should have substantial experience with at least one or two major molecular biology software packages, either for sequence analysis or molecular modeling. 
The experience of learning one of these packages makes it much easier to learn to use other software quickly.

4. Should be comfortable working in a command-line computing environment. Working in Linux or UNIX will provide this experience.

5. Should have experience with programming in a computer language such as Java, Unix, C, C++, RDBMS such as Oracle and Sybase, CORBA, Perl or Python, CGI and web scripting.

Chronological History of Bioinformatics

A Chronological History of Bioinformatics:

Bio-informaticians and students of Bioinformatics must know "Chronological History of Bioinformatics" Bioinformatics is multi-disciplinary field for finding solutions of problems in BIOLOGY by using computer software and tools. 

A Chronological History of Bioinformatics:

• 1953 - Watson & Crick proposed the double helix model for DNA based x-ray data obtained by Franklin & Wilkins.

• 1954 - Perutz's group develop heavy atom methods to solve the phase problem in protein crystallography.

• 1955 - The sequence of the first protein to be analysed, bovine insulin, is announed by F.Sanger.

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• 1969 - The ARPANET is created by linking computers at Standford and UCLA.

• 1970 - The details of the Needleman-Wunsch algorithm for sequence comparison are published.

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• 1972 - The first recombinant DNA molecule is created by Paul Berg and his group.

• 1973 - The Brookhaven Protein DataBank is announeced (Acta.Cryst.B,1973,29:1764). Robert Metcalfe receives his Ph.D from Harvard University. His thesis describes Ethernet.

• 1974 - Vint Cerf and Robert Khan develop the concept of connecting networks of computers into an "internet" and develop the Transmission Control Protocol (TCP).

• 1975 - Microsoft Corporation is founded by Bill Gates and Paul Allen. Two-dimensional electrophoresis, where separation of proteins on SDS polyacrylamide gel is combined with separation according to isoelectric points, is announced by P.H.O'Farrel.

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• 1988 - The National Centre for Biotechnology Information (NCBI) is established at the National Cancer Institute. The Human Genome Intiative is started (commission on Life Sciences, National Research council. Mapping and sequencing the Human Genome, National Academy Press: wahington, D.C.), 

• 1988- The FASTA algorith for sequence comparison is published by Pearson and Lupman. A new program, an Internet computer virus desined by a student, infects 6,000 military computers in the US.

• 1989 - The genetics Computer Group (GCG) becomes a privatae company. Oxford Molceular Group,Ltd.(OMG) founded, UK by Anthony Marchigton, David Ricketts, James Hiddleston, Anthony Rees, and W.Graham Richards. Primary products: Anaconds, Asp, Cameleon and others (molecular modeling, drug design, protein design).

• 1990 - The BLAST program (Altschul,et.al.) is implemented. Molecular applications group is founded in California by Michael Levitt and Chris Lee. Their primary products are Look and SegMod which are used for molecular modeling and protein deisign. InforMax is founded in Bethesda, MD. The company's products address sequence analysis, database and data management, searching, publication graphics, clone construction, mapping and primer design.

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• 1991 - The research institute in Geneva (CERN) announces the creation of the protocols which make -up the World Wide Web. The creation and use of expressed sequence tags (ESTs) is described. Incyte Pharmaceuticals, a genomics company headquartered in Palo Alto California, is formed. Myriad Genetics, Inc. is founded in Utah. The company's goal is to lead in the discovery of major common human disease genes and their related pathways. The company has discovered and sequenced, with its academic collaborators, the

following major genes: BRCA1, BRACA1 , CHD1, MMAC1, MMSC1, MMSC2, CtIP, p16, p19 and MTS2.

• 1993 - CuraGen Corporation is formed in New Haven, CT. Affymetrix begins independent operations in Santa Clara, California.

• 1994 - Netscape Communications Corporation founded and releases Naviagator, the commerical version of NCSA's Mozilla. Gene Logic is formed in Maryland. The PRINTS database of protein motifs is published by Attwood and Beck. Oxford Molecular Group acquires IntelliGenetics.

• 1995 - The Haemophilus influenzea genome (1.8) is sequenced. The Mycoplasma genitalium genome is sequenced.

• 1996 - The genome for Saccharomyces cerevisiae (baker's yeadt, 12.1 Mb) is sequenced. The prosite database is reported by Bairoch, et.al. Affymetrix produces the first commerical DNA chips.

• 1997 - The genome for E.coli (4.7 Mbp) is published.Oxford Molecualr Group acquires the Genetics Computer Group. LION bioscience AG founded as an intergrated genomics company with strong focus on bioinformatics. The company is built from IP out of the European Molecualr Biology Laboratory (EMBL), the European Bioinformtics Institute (EBI), the GErman Cancer Research Center (DKFZ), and the University of Heidelberg.paradigm Genetics Inc., a company focussed on the application of genomic technologies to enhance worldwide food and fiber production, is founded in Research Triangle Park, NC. deCode genetics publishes a paper that described the location of the FET1 gene, which is responsible for familial essential tremor, on chromosome 13 (Nature Genetics).

• 1998 - The genomes for Caenorhabitis elegans and baker's yeast are published.The Swiss Institute of Bioinformatics is established as a non-profit foundation.Craig Venter forms Celera in Rockville, Maryland. PE Informatics was formed as a center of Excellence within PE Biosystems. This center brings together and leverges the complementary expertise of PE Nelson and Molecualr Informatics, to further complement the genetic instrumention expertise of Applied Biosystems.Inpharmatica, a new Genomics and Bioinformatics company, is established by University College London, the Wolfson Institute for Biomedical Research, five leading scientists from major British academic centres and Unibio Limited. GeneFormatics, a company dedicated to the analysis and predication of protein structure and function, is formed in San Diego.Molecualr Simulations Inc. is acquired by Pharmacopeia.

• 1999 - deCode genetics maps the gene linked to pre-eclampsia as a locus on chromosome 2p13.

• 2000 - The genome for Pseudomonas aeruginosa (6.3 Mbp) is published. The Athaliana genome (100 Mb) is secquenced.The D.melanogaster genome (180 Mb) is sequenced.Pharmacopeia acquires Oxoford Molecular Group.

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• 2001 - The huam genome (3,000 Mbp) is published.