Bioinformatics


Gharip Biotech channel is an educational site for sharing Knowledge, it is very unique because it collect the BIOTECHNOLOGY science in one site.


this educational activities has been dedicated to spirit of my mother


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Molecular Immunology

Actually, it is a discussion of the most famous book in the category of molecular immunology.

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Molecular Biology Lab

Concerning the techniques and laboratory skills in the molecular biology lab.

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Molecular Biology Theory

Discussing the basic concepts of molecular biology theories.

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Introduction


This course teach you the basics of Bio-Informatics.

It is under construction, it suspected to be 6 Modules.

Every Module contain various Sessions.

This work is dedicated for spirit of mother.



Module 1 Session 1



bioinformatics def

download this slides and transcripts in-order to get major view of what this video talk about .

Bioinformatics –A Definition
provide an introduction to the field of bioinformatics, with a focus on important bioinformatics tools, algorithms and resources.

use a combination of theoretical and practical sessions for participants to gain practical experience in using various tools and resources.

aimed at individuals from a molecular biological background who have a basic understanding of biochemistry and/or genetics and would like to become bioinformatics users.

A base line level of the understanding of the central dogma of biology is a requirement.

Molecular biology YouTube

Molecular biology telegram
https://t.me/joinchat/NdMx3kOHYqveRTk2fYVx_Q

Molecular biology Web site
https://wp.me/Pc3aQN-5

Facebook
https://www.facebook.com/ali.gharip.733

hello@example.com







Biological Databases and Resources NCBI

Resources of Scientific Literature


Boolean operators symbols


Advance Searching in PubMed


MeSH terms


Searching Specific Paper in NCBI



Question of Module 1 – Session 2

Each of the following examples should be conducted as individual search! Copy and paste the search query that you generated for each search and the number of results for questions 1 – 6.

Example of a search query and number of results : ((FOXP2[Title/Abstract]) AND mutation[Title/Abstract]) AND language disorders[Title/Abstract] – 12 results

  1. Any article dealing with ostrich
  2. Articles authored by T Hubbard (Careful: do you put this as Hubbard T or T Hubbard?)
  3. Articles authored since 2003 by the T Hubbard who works at the Sanger Institute
  4. An article by H.H.Erdemir published in 2014 in the journal J Biol Chem
  5. Articles about schizophrenia risk (mentioned in the title), published in a journal called Epigenomics, written by authors from the University of Cambridge. Provide the citation/s in plain text format.
  6. You would like to conduct a search for articles about cancer in children. Search the MeSH database at NCBI to find out what the best keywords are to use for both cancer and children when building up your search query.

Filters

Before setting any filters, using the advanced search page, search for papers that deal with myopia.

  • Copy and paste your search query. How many papers are found?

Now set Filters to limit the search to clinical trials involving human males and where there are links to free full text papers. How many papers do you retrieve once the filters have been set?

  • Summarise the difference between setting restrictions using Filters and using the features of the advanced search page?

Remember Filters remain set until they are turned off!

Other features

  • Bring up the details of the papers found in the last search you did by clicking on the number of papers found.
  • Look at the options for sending output to a file, to text, to email and so on.
  • Select the top 3 papers. Add them to the clipboard. Check under Clipboard to see them.

 

MyNCBI

Go to MyNCBI and register http://www.ncbi.nlm.nih.gov/sites/myncbi/. There are tutorials on how to use this. The most useful features are:

  • Saving search results. Once registered and logged in you can create and save search results to specific collections. This is useful since you are able to create collections to store the search results for different aspects of your research.
  • Saving search queries. Useful if you wish to run the same or related searches over a period of time.
  • Saving BLAST search results and options used. i.e. the particular BLAST program used, the parameters, the database searched and the query sequence


Module 1 – Session 3


IT begin yet

UniProt Mapping Tool




Module 1 Session 4 practical assignment



Module 1 Session 4 practical assignment


Module 2 Session 1 practical assignment


Module 2 Session 2 practical assignment


Module 2 linux session 3, while loop syntax


tricky wiky in linux



Module 3 Session 1 practical assignment


Global and Local alignment


Module 3 Session 3 practical assignment


Module 3 Session 3 practical assignment


Module 3 Session 3 practical assignment


Jalview program for Multiple Sequence Alignment

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