z-Bioinformatics

8/3/2019 z-Bioinformatics

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ContentWhat is bioinformatics.

What is computational Biology.

Data mining.Application of data mining.

Net accessible resources.

Sequence Analysis.

What can be Done with sequence

Analysis.?Identification of protein primary

sequence from DNA sequence.

Tips for searching Database.The process of Evolution.

Principle and their Importance.Conclusion.


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What is Bioinformatics.

Bioinformatics describe anyuse of computer to handle

biological information. Inpractice, the definition usedby most people in narrower,bioinformatics to them is asyononym for

computational molecularbiology, the use of

computers to characterizethe molecular components

of living.


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What is data mining.

Data mining is the process bywhich testable hypothesis aregenerated regarding the function

or structure of gene or proteinof interest by idenfenite similarsequence in better characterized

organism. Application of data mining:- Include fraud detection, credit

card scoring and personal profilemarketing. Skillful interpretationof data can enhance customerrelation, direct marketing, trendanalysis, financial marketforecasting and international

criminal investigations.


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Net accessible resources:-

Two main world wide web sites

provide information on data mining:- The data mine: This includes

pointers to FTP-able papers, and two

large data mining bibliographies. Itattempts to provide links to as muchof the available data mining

information on the net as is possible.Run by Pryke , at the University ofBirmingham.

Knowledge discovery mine: Theknowledge discovery mine has theKDD FAQ, a comprehensive catalog

of tools for discovery in data ,as wellas back issues of the KDD-Nuggetmailing list. Run by leading KDD

researcher Gregory Piatetsky-Shapiro.


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What is sequence Analysis.

Sequence analysis is the processof trying to find out somethingabout a nucleotide or amino acid

sequence, employing in silicobiology techniques. You may havesequenced a gene yourself, and

wish to learn what the long string ofletters representing base, actuallycode for. You may want to confirmthat you indeed cloned a genesuccessfully, or you might want to

learn about a sequence of DNA thatyou know absolutely nothing about.You may want to know if a worm

has a similar protein to a humanone..

Wh t b d ith


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What can be done now with

sequence Analysis

Given the pessimistic view ofsequence analysis presented in theprevious section, why do we even

bother with it? In the first place theattempted to find methods forsuccessful sequence analysis is a

research goal in its own right; onewhose potential rewards are sovast as to make it of the first

importance. In the second place,although there are many thingsthat sequence analysis cannot yet

do , there are many very worthwhile things that can currently bedone with sequence analysis and

these will be summarized in thissection.


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Identification of protein sequence

from DNA sequence The computer programs which are used to infer

protein sequence from DNA sequence provideinformation which can be used to be helpapproach a solution. For example, if you are

trying to find out in a DNA sequence a protein isencoded, it is very used to know what peptideswould be encoded by all six reading frames. Astretch containing many stop codons is a poor

candidate for encoding a protein. This will notabsolutely tell you where the protein sequencestarts and stops, but it will you guess where thatmight occur. Programs exist for doing these . In

fact there are many factors you can used toguess where in a DNA sequence a proteinsequence might reside; use of the expectedcodon bias, presents of characteristic sequences

representing regulatory signals in the DNA andso forth. One family of programs integrates avariety of these approaches , and using eitherexplicit algorithms or trained neural nets ,makes

a prediction.


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Tips for searching database.

Use latest database version Use blast first, then a finer tool (fasta,

search, blitz , sweep, block et al) Search both strands when using FASTA.

This is automatically done in GCG Program. Translate sequence where relevant

Search 6-frame translation of DNAdatabase

EO200 for protein

If the query has repeated segments, deletethem and repeat search


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The process of evolution.

Indeed, homologous proteins arisefrom mutations in a common

ancestor coding gene. Through theprocess of gene divergence, somegene mutations have been

accepted by natural selectionbecause they preserved the foldingand function of the coded protein.

This could be represented byschematic tree where several genescome from a common ancestorgene.


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Principle and their

importance Sensitivity Versus Specificity

There are different ways toestimate similarity between twosequences, allowing us to modify

the sensitivity and specificity ofthe results when performing asequence database search with a

query sequences . If thesensitivity is high, more distantlyrelated sequence as the S.griseus protease will beretrieved.


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Continue..

However, unrelated sequences

as the endochitinase will also bereturned. On the other hand if thespecificity is high , only closely

related sequences will bereturned but, in this case,distantly related ones will be

missed . Thus, a researcher hasto know how he could managethis problem .And this is one

additional reason explaining whybiologists should not treatsoftware as a black box .


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Window approaches In particular, in comparing two

sequences, a dot matrix can be used

where one sequence is written outhorizontally and the other is writtenout vertically . A dot I placed at the

intersection of a row and a column foreach matched pair of letters. If thefrequency matched letters betweentwo sequences is high, particularly inDNA sequences , which arecomposed of only four buildingblocks , the background noise is

high . In order to reduce the noise,one can place a dot only when severaljoined letters are matched. The

numbers of joined letters evaluatedtogether is called the window size.


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Efficient use of program When performing a database

search , a research must knowthat he can improve his results .If he knows the principles, the

use of windows, he will beincrease the sensitivity bydecreasing the window size

parameter. This will improve theability of the program torecognize distantly related

sequences . Alternatively , he willbe able to increase the specificityby increasing the window size

parameter ..


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conclusion

This is important for a researcherwho wants to use the programs

available for sequence analysisto acquire a reliable knowledgeof biocomputing. Knowing thecapabilities and the draw backsof the program will help us to

use them in a more accurate andefficient way.

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