NCBI tools in Linux
What you'll learn
- NGS
- NCBI blast tools
- Clustalw
- SRA tools
- some Biopython
- primer3
- GeoR
Requirements
- basic knowledge of Linux programming and molecular biology
Description
Bioinformatics has become an entirely independent discipline. This branch of science can greatly speed up and facilitate biological and biomedical research. As a biology or medical student or researcher you might be using bioinformatics tools at NCBI. You might also be interested in learning how to use these programs in Linux to make your work more efficient by automating them. This course helps you do exactly this.
In this course we will learn how to use the Linux version of several NCBI tools, such as ClustalW, bl2seq, analyzing GEO data sets, primer design by primer3, or downloading sequences using a Biopython script. We will also learn how to format BLAST databases and run Blast queries against them. We will also learn about the SRA database and how to download SRA NextGen fastq data sets.
In order to take this course some knowledge of Linux is required. For example we will write a shell script and a python script in one of the videos. You also have to know how to navigate in a Linux environment and run commands, but it should not be too difficult.
I hope that the knowledge that you gain in this course will help you become a more effective researcher.
Have fun!
Who this course is for:
- biology and bioinformatics students
Instructor
- 4.3 Instructor Rating
- 74 Reviews
- 368 Students
- 5 Courses
Education
· Biology, MS (ELTE-TTK, 2003) (thesis: Miklos Cserzo, Agricultural Biotechnology Center, Godollo, bioinformatics group)
· PhD in Bioinformatics (SZTE-TTIK, 2011) SZTE TTIK, BRC-HAS, Szeged, 2011(thesis: Janos Gyorgyey)
· Software Developer, BSc (SZTE-TTIK, 2010) (thesis: Tamas Gergely, dept. of software development)
Academic work history
· Bioinformatics Programmer, Fulgent Genetics, Temple City, CA (2020-present)
· Bioinformatics Programmer, University of Texas at San Antonio, Health Science Center (UTHSCSA), San Antonio (2018-2019)
· Bioinformatics Programmer, University of Nebraska Medical Center (UNMC), Omaha (2013-2017)
· Post-doctoral Research Associate, University of Nebraska-Lincoln (UNL) (2011-2013)
· ELTE TTK University, Institute of Chemistry, Laboratory for Chemical Kinetics, Budapest (2010-2011)
· Biological Research Center (BRC), Szeged, Plant Cell Division Cycle and Stress Adaptation group (2003-2010)