Bioinformatics Practical Course

Bioinformatics Practical Course
Only in Ramadan !
Original Price
Offer Price
50% discount for Bioinformatics Practical Course !

ATIT Academy announces a special discount for students for the course Bioinformatics Practical Course.

This course will be online via Skype and TeamViewer in a smart room with high-quality equipment, so the students can interact with the teacher as if he was in the academy!


Terms & Conditions:

  1. To reserve the seat you must register and pay during the discount period

  2. A smart room equipped with high-quality equipment

  3. Appointments will be set in the first lecture to suit everyone

  4. The ability to register online via Skype and Teamviewer

  5. Each student will get a certificate signed and stamped by the Academy at the end of the course.

  6. The possibility of taking the course (Private) so that the student can choose the appropriate papers for his/her specialization and research

This offer is available during Ramadan only, be quick to register and book your seat now!

Table of content:

1. Bioinformatics databases

1.1. Introduction

1.1.1. Motivation

1.1.2. Central dogma of life

1.1.3. Type of bioinformatics databases

1.2. Nucleotide sequence databases

1.2.1. EMBL

1.2.2. GeneBank

1.2.3. DDBJ

1.3. Protein amino acid sequence databases

1.3.1. How protein sequences are determined DNA/mRNA coding Edman degradation reaction Mass spectrometry

1.3.2. SwissProt/TrEMBL

1.3.3. PIR

1.3.4. UniProt UniProtKB/Swiss-Prot and UniProtKB/TrEMBL UniParc UniRef

1.4. Protein structure databases

1.4.1. History of structural biology

1.4.2. Protein Data Bank

1.4.3. SCOP

1.4.4. CATH

1.5. Protein function databases

1.5.1. Pfam-protein family database

1.5.2. GO-gene ontology

1.5.3. PROSITE-protein function pattern and profile

1.5.4. ENZYME-Enzyme commission

1.5.5. BioLiP-ligand protein binding interaction 

2. Pair-wise sequence alignments and database search

2.1. Biological motivation-why sequence alignment?

2.2. What is a sequence alignment?

2.2.1. Scoring matrix PAM BLOSUM

2.2.2. Gap penalty

2.3. Dynamics programming

2.3.1. Needleman-Wunsch: global alignment algorithm

2.3.2. Smith-Waterman: local alignment algorithm

2.3.3. Gotoh algorithm 

2.4. Heuristic methods

2.4.1. FASTA

2.4.2. BLAST

2.5. Statistics of sequence alignment score

2.5.1. E-Value

2.5.2. P-Value

3. Phylogenic tree & multiple sequence alignments

3.1. Neighbor-joining method and phylogenetic tree

3.2. How to construct multiple sequence alignments?

3.2.1. ClustalW

3.2.2. PSI-BLAST PSI-Blast pipeline Profile pseudocount PSSM-position specific scoring matrix Installing and running PSI-Blast programs Interpret PSI-Blast out

3.2.3. Hidden Markov Models Viterbi algorithm HMM based multiple-sequence alignment Creating HMM by iteration HMMER SAM

3.3. Sequence profile & profile based alignments

3.3.1. What is sequence profile?

3.3.2. Henikoff weighting scheme

3.3.3. Profile-to-sequence alignment

3.3.4. Profile-to-profile alignment

4. Protein structure alignments

4.1. Structure superposition versus structural alignment

4.2. Structure superposition methods

4.2.1. RMSD

4.2.2. TM-score

4.3. Structure alignment methods

4.3.1. DALI

4.3.2. CE

4.3.3. TM-align

4.4. How to define the fold of proteins?

4.5. Number of protein folds in the PDB

5. Protein secondary structure predictions

5.1. What is protein secondary structure?

5.2. Hydrogen bond

5.3. How to define a secondary structure element?

5.4. Basics of machine learning and neural network methods

5.5. Methods for predicting secondary structure

5.5.1. Chou and Fasman method

5.5.2. PHD

5.5.3. PSIPRED

5.5.4. PSSpred