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- What is Bioinformatics.
- Bioinformatics Vs. Medical Informatics.
- Central Dogma of Life.
- DNA, Genomes.
- RNA, Transcriptomes.
- Proteins, Proteomics.
- Transcriptions and Translation.
- Omics era.
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- Bioinformatics Road.
- Prepare a sequencing library.
- Sequencing Technologies.
- Sequencing by Synthesis.
- Base Caller.
- Nanopore Sequencing.
- Single Molecule Real Time Sequencing.
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- Key attributes of Different Sequencing Technologies
- Sequencing Projects.
- Egyptian Genome Project.
- Whole Genome Vs. Whole Exome Vs. Targeted Sequencing
- Sequencing Services: RNA-seq, Bisulfite, ChIP-seq, Single cell sequencing
- Paired-end Vs. Single-end reads
- Genomic Coverage
- Base Qualities
- FASTA Vs. FASTQ data files format
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- Genome Annotations
- Genome Annotations Data File Formats: BED, GFF, GFF3
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- String Definitions: String, substring, prefix, suffix, subsequence, kmers
- The exact marching string problem
- NAÏVE Algorithm for pattern matching
- NAÏVE Algorithm Running Time Complexity Analysis
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- Boyer Moore Algorithm
- Boyer Moore Algorithm: Bad Character Rule
- Boyer Moore Algorithm: Good Suffix Rule
- Boyer Moore Algorithm: Strong Good Suffix Rule
- Boyer Moore Algorithm: All togther
- Boyer Moore Algorithm Running Time Complexity Analysis
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7 |
- Knuth Morris Pratt Algorithm
- Knuth Morris Pratt Algorithm: LPS
- Knuth Morris Pratt Algorithm Running Time Complexity Analysis
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- Rabin-Karp Algorithm
- Rabin-Karp Algorithm: string hashing
- Rabin-Karp Algorithm Running Time Complexity Analysis
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- Sequence Alignment
- Scoring an Alignment
- Different Scoring Schemes & Scoring Matrics: To be continue in the next lecture
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- Different Scoring Schemes & Scoring Matrics
- Local Vs. Global Sequence Alignments
- Pairwise Vs. Multiple Sequence Alignments
- Linear Vs. Affine Gap penality Models.
- Global Piarwise Sequence Alignment Algorithm: Needleman-Wunsch
- Local Piarwise Sequence Alignment Algorithm: Smith-Waterman
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- Sequence Assembly
- Sequence Assembly Challenges
- Sequence Assembly Terminologies
- Comparative Vs. De Novo Assembly
- Overlap-Layout-Consensusly Genome Assembly Approach: To be continue in the next lecture
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- Overlap-Layout-Consensusly Genome Assembly Approach
- Greedy Graph Genome Assembly Approach
- De-Bruijn-Graph Genome Assembly Approach
- Genome Assembly Evaluation Metrics
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13 |
- Task1: Code a whole Boyer Moore Algorithm using Good Suffix Rule and Bad Character Rule, prepare a video to explain it.
- Course Project: up to students to choose thier project ideas and prepare a video to explain its implementation.
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