من انا

صورتي
الرياض, Saudi Arabia
مسلم، وأناأحوج ما أكون إلى معرفة نفسي

الثلاثاء، 31 يناير، 2012

Bioinformatics

Bioinformatics
      Bioinformatics is the application of computer science and information technology to the field of biology and medicine.
      Bioinformatics was applied in the creationخلق and maintenance  المحافظةof a database to store biological information at the beginning of the "genomic revolutionالثورة ", 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 both access existing data as well as submit new or revised data.
• تطوير هذا النوع من قاعدة البيانات المعنية ليست الهدف الوحيد من التصميم لتطوير واجهات معقدة حيث تمكن الباحثون من الوصول إلى البيانات الموجودة على حد سواء وكذلك تقديم البيانات الجديدة أو المنقحة.

      Bioinformatics is about searching biological databases, comparing sequences, looking at protein structures, and (more generally) asking biological and biomedical questions with a computer.
Bioinformatics is about finding and interpreting biological data online.
bioinformatics   يكون حول البحث في قواعد البيانات البيولوجية  ، وبمقارنة تسلسل ، والنظر في تراكيب البروتين، و (بشكل عام) البيولوجية والطبية الحيوية مع طرح الأسئلة على جهاز الكمبيوتر.bioinformatics   هو يكون حول حقائق بيولوجية وتفسير البيانات على الانترنت.

Retrieving DNA Sequences
Not all DNA is coding for protein
q  Various types of DNA sequences are involved in defining a gene:
ü Regulatory regions (usually preceding the coding region)
ü  Untranslated regions that precede and follow the coding regions
ü  The protein-coding region

      In eukaryotes (yeast, plants, animals), the protein-coding region is divided into a variable number of exons — gene segments that contribute to the final protein — interspersed with introns — gene segments that do not.
      As a consequence, working with DNA sequences is always trickier than working with protein sequences.



Messenger RNA

Prokaryotic mRNA



Open reading frame

                                                      In molecular genetics, an open reading frame (ORF) is a DNA sequence that does not contain a stop codon in a given reading frame.

Using Nucleotide Sequence Databases
      Sequence databases are great tools because they offer a unique window on the past.
      They make it possible to answer today’s biological questions by enabling us to analyze sequences that may have been determined as many as 25 years ago.

      By doing this, they connect past and present molecular biology.

GeneBank
      GenBank is the leading nucleotide sequence repository maintained as a consortium between the U.S. National Center for Biotechnology Information (NCBI), the European Molecular Biology Laboratory (EMBL), and the DNA Data Bank of Japan (DDBJ).
     Point your browser to www.ncbi.nlm.nih.gov/entrez/












Creating Multiple Alignment
                     Get ClustalX2.11 from:

Phylogenetic Analysis
q  Methods for constructing Phylogenies:
1.      Neighbor Joining (NJ).
2.      Maximum Parsimony (MP).
3.      Maximum Likelihood (ML).
4.      Bayesian (BAY).


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Using PAUP* to creat a tree


Becoming an Instant Expert with PubMed/Medline
      Searching PubMed
      Using your favorite Internet browser, navigate to:
Enter Key words


Retrieving Protein Sequences
      Protein sequences are simple objects with a relatively narrow range of sizes (they are about 300 amino acids long, plus or minus 200, except for a few giant ones), clearly defined boundaries, and specific functional attributes.
      Furthermore, proteins of microbes or higher eukaryotes (animal and plants) have roughly the same properties.




ExPASy: A prime Internet site for protein information
      Created and managed by one of the pioneers of protein bioinformatics, Prof. Amos Bairoch, the ExPASy server is a world-leading resource for protein information.
      In addition to the Swiss-Prot protein sequence database, the ExPASy site provides numerous analysis tools that you can use.





ExPASy
      Point your browser to www.expasy.org/sprot/


Retrieving the DNA sequence relevant
to my protein
     www.expasy.org/sprot/
     Cross-references

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