Bioinformatics Questions and Answers

1. Questions & Answers on Sequence Alignment

The section contains questions and answers protein motfis, motif and domain databases using regular expressions and statistical models, protein family databases, global and local sequence alignment, dot matrix sequence comparison and bayesian statistics.

Protein Motifs and Domain Prediction Motif and Domain Databases Using Regular Expressions Motif and Domain Databases Using Statistical Models  Protein Family Databases Global Sequence Alignment Local Sequence Alignment

Motif Discovery in Unaligned Sequences Dot Matrix Sequence Comparison Dynamic Programming Algorithm for Sequence Alignment Use of Scoring Matrices and Gap Penalties in Sequence Alignments Assessing the Significance of Sequence Alignments Bayesian Statistics

2. Questions on Pairwise Sequence Alignment

The section contains questions on sequence homology versus sequence similarity, methods and statistical significance of sequence alignment.

Sequence Homology Versus Sequence Similarity and Identity Methods

Statistical Significance of Sequence Alignment

3. Questions & Answers on Multiple Sequence Alignment

The section contains questions and answers on exhaustive and heuristic algorithms, wunsch algorithm, progressive and iterative methods of multiple sequence alignment, sequences localized alignment, aiding alignment statistical methods and specific scoring matrices.

Exhaustive Algorithms Heuristic Algorithms Needleman – Wunsch Algorithm Progressive Methods of Multiple Sequence Alignment

Iterative Methods of Multiple Sequence Alignment Localized Alignments in Sequences Statistical Methods for Aiding Alignment Position – Specific Scoring Matrices

4. Questions on Database Similarity Searching

The section contains questions on heuristic database searching, blast, fasta, smith – waterman method, fasta and blast comparison.

Heuristic Database Searching Basic Local Alignment Search Tool (BLAST) FASTA

Comparison of FASTA and BLAST Database Searching with the Smith – Waterman Method

5. Questions & Answers on Structural Bioinformatics

The section contains questions and answers on protein structure basics and structural visualization, protein structure comparison and classification.

Protein Structure Basics Protein Structural Visualization

Protein Structure Comparison Protein Structure Classification

6. Questions on Secondary Structure Prediction

The section contains questions on protein secondary structure prediction, secondary structure and coiled coil prediction.

Protein Secondary Structure Prediction for Globular Proteins Secondary Structure Prediction for Transmembrane Proteins

Coiled Coil Prediction

7. Questions & Answers on Protein Tertiary Structure Prediction

The section contains questions and answers on ab initio protein structural prediction, threading and fold recognition.

Ab Initio Protein Structural Prediction & Homology Modeling

Threading and Fold Recognition

8. Questions on RNA Structure Prediction

The section contains questions on rna structures, rna secondary structure prediction methods, ab initio and comparative approach, performance evaluation, prediction limitations, energy method and free grammars, rna genomes and rna structure modeling applications.

Types of RNA Structures RNA Secondary Structure Prediction Methods Ab Initio Approach Comparative Approach Performance Evaluation

Limitations of Prediction Minimum Free – Energy Method & Stochastic Context – Free Grammars MFOLD and the Use of Energy Plots Searching Genomes for RNA & RNA Structure Modeling Applications

9. Questions & Answers on Genome Mapping, Assembly and Comparison

The section contains questions and answers on genome mapping and sequencing, genome sequence assembly, genome annotation and comparative genomics.

Genome Mapping Genome Sequencing Genome Sequence Assembly

Genome Annotation Comparative Genomics

10. Questions on Functional Genomics & Proteomics

The section contains questions on sequence and microarray based approaches, sage and dna microarrays comparison, protein expression analysis, post translational modification, protein sorting and interactions.

Sequence – Based Approaches Microarray-Based Approaches Comparison of SAGE and DNA Microarrays Technology of Protein Expression Analysis

Post Translational Modification Protein Sorting Protein Interactions

11. Questions & Answers on Molecular Phylogenetics

The section contains questions and answers on phylogenetics basics, tree representation forms, gene phylogeny versus species phylogeny.

Phylogenetics Basics Gene Phylogeny Versus Species Phylogeny

Forms of Tree Representation

12. Questions on Phylogenetic Tree Construction Methods and Programs

The section contains questions on distance and character based methods, phylogenetic tree evaluation and programs, maximum parsimony method, maximum likelihood approach and reliability of phylogenetic predictions.

Distance Based Methods Character Based Methods Phylogenetic Tree Evaluation Phylogenetic Programs

Maximum Parsimony Method The Maximum Likelihood Approach Reliability of Phylogenetic Predictions

13. Questions & Answers on Gene and Promoter Prediction

The section contains questions and answers on gene prediction programs categories, gene prediction in prokaryotes and eukaryotes.

Categories of Gene Prediction Programs Gene Prediction in Prokaryotes

Gene Prediction in Eukaryotes – 1 Gene Prediction in Eukaryotes – 2

14. Questions on Promoter and Regulatory Element Prediction

The sections covers questions on prediction algorithms, promoter and regulatory elements in prokaryotes & eukaryotes.

Promoter and Regulatory Elements in Prokaryotes & Eukaryotes Prediction Algorithms – 1

Prediction Algorithms – 2 Prediction Algorithms – 3

15. Questions & Answers on Predicting the Structure of Protein – Biomolecular Interactions

The section contains questions and answers on molecular complementarity, conformational flexibility, evaluation of models & visualization methods.

Molecular Complementarity Conformational Flexibility

Evaluation of Models & Visualization Methods

16. Questions on Global Approaches for Studying Protein – Protein Interactions

The section contains questions on protein and domain interactions, gene order use and phylogeny to predict protein.

Protein – Protein Interactions Structural Analyses of Domain Interactions

The Use of Gene Order & Phylogeny to Predict Protein – Protein Interactions

17. Questions & Answers on Predicting the Structure of Protein – Biomolecular Interactions

The section contains questions and answers on dna and genomic sequencing, cdna libraries of expressed genes, sequence formats and storage, database access program, genemo anatomy, comparative genomics, sequence assembly and gene identification.

DNA & Genomic Sequencing Sequencing cDNA Libraries of Expressed Genes & Submission of Sequences to the Databases Sequence Formats & Computer Storage of Sequences Multiple Sequence Formats, Storage of Information in a Sequence Database Using the Database Access Program ENTREZ Genome Anatomy – 1 Genome Anatomy – 2

Genome Anatomy – 3 Sequence Assembly and Gene Identification – 1 Sequence Assembly and Gene Identification – 2 Sequence Assembly and Gene Identification – 3 Comparative Genomics – 1 Comparative Genomics – 2

18. Questions on Genome Analysis

The section contains questions on genes functional classification, global gene regulation and gene function prediction.

Functional Classification of Genes Global Gene Regulation

Prediction of Gene Function Based on a Composite Analysis