BIF501 Handouts Complete

Sr. No. Title Applications of Bioinformatics-I Applications of Bioinformatics-II Nucleotide Sequence databases Protein databases Genome and organism specific databases Gene expression databases Medical databases Sequence submission DNA Sequence Retrieval Protein Sequence Retrieval Sequence Formats Data Retrieval Genome Informatics Prokaryotic Genome Eukaryotic Genomes Epichromosomal elements (EEs) Genome repeats Transposable Elements (TEs) Eukaryotic Gene Structure Comparative Genomics Comparative Proteomics Between proteome comparison Horizontal Gene Transfer Gene Order (Synteny) Genome annotations Genome Sequencing Structure of RNA DNA Transcription Protein Translation Dynamic Programming I Dynamic Programming II Algorithm for Dynamic Programming Restriction Mapping I Restriction Mapping II Partial Digest Problem Practical Restriction Mapping Algorithm Partial Digest Algorithm I Partial Digest Algorithm II Regulatory Motifs in DNA Sequences Profiles I Profiles II Profiles III Motif Finding Problem I Motif Finding Problem II Search Trees – Introduction Search Trees – Best Alternative Algorithm for Search Trees I Algorithm for Search Trees II Next Vertex Algorithm What is an algorithm Bypass Algorithm Finding Motifs Simple Motif Search Algorithm Branch and bound Algorithm Brute Force Median Search Genome Rearrangements A greedy approach to motif finding The Power of DNA Sequence Comparison Brute Force vs Greedy Algorithm Sequence Similarity Edit Distance Alignment Edit Graph I Edit Graph II Longest Common Sequences I Recurrence for LCS problem Algorithm for LCS Scoring Alignments I Scoring Alignments II PAM matrix Local Sequence Alignment I Local Sequence Alignment II Local Alignment Problem Progressive Multiple Alignment Gene Prediction I Gene Prediction II one Approach for Gene Prediction Second Approach for Gene Prediction Statistical Approach to Gene Prediction I Statistical Approach to Gene Prediction II Statistical Approach to Gene Prediction III Similarity based Approached to Gene Prediction I Similarity based Approached to Gene Prediction II ORF Prediction ORF Finders TSS Prediction Prediction of Splice Junctions Prediction of Exons Annotation of assembled Genome