Introduction to Bio

BIO-INFORMATICS GROUP-1

JALPAIGURI GOVERNMENT ENGINEERING COLLEGE

Computer Science and Engineering

BIO-INFORMATICS 06/16/2015

GROUP-1 1

Table Of Contents

Bioinformatics-Introduction

What Is Bioinformatics?

What is Cell?

Basic Structure of Cell

Types of cell

What is DNA?

What is RNA?

What is Protein?

The Central Dogma

Analyzing Protein Sequences

A brief history of sequence analysis

Reading protein sequences from N to C

Working with protein 3-D structures

Protein bioinformatics covered

Analyzing DNA Sequences

Reading DNA sequences the right way

The two sides of a DNA sequence

Palindromes in DNA sequences

Analyzing RNA Sequences

RNA structures: Playing with sticky strands

More on nucleic acid nomenclature


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DNA Coding Regions: Pretending to Work with Protein Sequences

Turning DNA into proteins: The genetic code

More with coding DNA sequences

DNA/RNA bioinformatics covered

Working with Entire Genomes

Genomics

How Most People Use Bioinformatics

Becoming an Instant Expert with PubMed/Medline

Finding out about a protein by its name

Searching PubMed using authors names

Searching PubMed using fields

Searching PubMed using limits

A few more tips about PubMed

Retrieving Protein Sequences

More advanced ways to retrieve protein sequences

Retrieving a list of related protein sequences

Retrieving DNA Sequences

Not all DNA is coding for protein

Going from protein sequences to DNA sequences

Retrieving the DNA sequence relevant to my protein

Using BLAST to Compare My Protein Sequence

Using Nucleotide Sequence Databases

Reading into Genes and Genomes

Prokaryotes: Small bugs, simple genes


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Eukaryotes: Bigger bugs, complex genes

Making Use (and Sense) of GenBank

Making sense of the GenBank entry of a prokaryotic gene

Making sense of the GenBank entry of an eukaryotic mRNA

Making sense of a GenBank eukaryotic genomic entry

Working with related GenBank entries

Retrieving GenBank entries without accession numbers

Using a Gene-Centric Database

Working with Whole-Genome Databases

Working with complete viral genomes

Working with complete bacterial genomes

More bacterial genomics at TIGR

Microbes from the environment at DoE

Exploring the Human Genome

Finding out about the Ensembl project

Using Protein and Specialized Sequence Databases

Protein Alignment: Often More Informative Than DNA Alignment

Definitions: Homology, Similarity, Identity

Gaps

Scoring Matrices

Dayhoff Model: Accepted Point Mutations

PAM1 Matrix, PAM250 and Other PAM Matrices

Practical Usefulness of PAM Matrices in Pairwise Alignment

Pairwise Alignment and Limits of Detection: The Twilight Zone


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Pairwise Alignment, Homology, and Evolution of Life

From Translated ORFs to Mature Proteins

ORFs: What we see is NOT what we get

A personal final destination for each protein

A combinatorial diversity of folds and functions

Name and origin of the protein

The References and Cross-References

Finally, the sequence itself

Finding Out More about our Protein

Finding out more about modified amino acids

Some advanced biochemistry sites

Finding out more about biochemical pathways

Finding out more about protein structures

Finding out more about major protein families

Working with a Single DNA Sequence

Catching Errors Before Its Too Late

Removing vector sequences

Cases when you shouldnt discard your sequence

Computing/Verifying a Restriction Map

Designing PCR Primers

Analyzing DNA Composition

Establishing the G+C content of our sequence

Counting words in DNA sequences

Counting long words in DNA sequences


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Experimenting with other DNA composition analyses

Finding internal repeats in our sequence

Identifying genome-specific repeats in our sequence

Finding Protein-Coding Regions

ORFing your DNA sequence

Analyzing your DNA sequence with GeneMark

Finding internal exons in vertebrate genomic sequences

Complete gene parsing for eukaryotic genomes

Analyzing your sequence with Genome Scan

Assembling Sequence Fragments

Managing large sequencing projects with public software

Assembling your sequences with CAP3

Working with RNA

Predicting, Modeling and Drawing RNA Secondary Structures

Noncoding RNA

Noncoding RNAs in the Rfam Database

Transfer RNA

Ribosomal RNA

Small Nuclear RNA

Small Nucleolar RNA

MicroRNA

Short Interfering RNA,

Using Mfold

Interpreting mfold results


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Forcing interaction in mfold

Searching Databases and Genomes for RNA Sequences

Finding tRNAs in a genome

Using PatScan to look for RNA patterns

Finding the New RNAs: miRNAs and siRNAs

Doing RNA Analysis for Free over the Internet

Studying evolution with ribosomal RNA

Finding the small, non-coding RNA we need

Generic RNA resources

Working with a Single Protein Sequence

Doing Biochemistry on a Computer

Predicting the main physico-chemical properties of a protein

Interpreting ProtParam results

Digesting a protein in a computer

Doing Primary Structure Analysis

Looking for transmembrane segments

Looking for coiled-coil regions

Predicting Post-Translational Modifications in Your Protein

Looking for PROSITE patterns

Interpreting ScanProsite results

Finding Known Domains in Your Protein

Choosing the right collection of domains

Finding domains with InterProScan

Interpreting InterProScan results


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Finding domains with the CD server

Interpreting and understanding CD server results

Finding domains with Motif Scan

Discovering New Domains in Your Proteins

More Protein Analysis for Free over the Internet

Similarity Searches on Sequence Databases

Understanding the Importance of Similarity

The Most Popular Data-Mining Tool Ever: BLAST

BLASTing protein sequences

Understanding your BLAST output

BLASTing DNA sequences

The BLAST way of doing things

Controlling BLAST: Choosing the Right Parameters

Controlling the sequence masking

Changing the BLAST alignment parameters

Controlling the BLAST output

Making BLAST Iterative with PSI-BLAST

PSI-BLASTing protein sequences

Avoiding mistakes when running PSI-BLAST

Discovering and using protein domains

with BLAST and PSI-BLAST

Similarity Searches for Free over the Internet

Comparing Two Sequences

Making Sure You Have the Right Sequences and the Right Methods


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Choosing the right sequences

Choosing the right method

Making a Dot Plot

Choosing the right dot-plot flavor

Using Dotlet over the Internet

Doing biological analysis with a dot plot

Making Local Alignments over the Internet

Choosing the right local-alignment flavor

Using Lalign to find the ten best local alignments

Interpreting the Lalign output

Making Global Alignments over the Internet

Using Lalign to Make a Global Alignment

Aligning Proteins and DNA

Free Pairwise Sequence Comparisons over the Internet

Building a Multiple Sequence Alignment

Finding Out if a Multiple Sequence Alignment Can Help You

Identifying situations where multiple alignments do not help

Helping your research with multiple sequence alignments

Choosing the Right Sequences

The kinds of sequences youre looking for

Gathering your sequences with online BLAST servers

Choosing the Right Method of Multiple Sequence Alignment

Using ClustalW

Aligning sequences and structures with Tcoffee


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Crunching large datasets with MUSCLE

Interpreting Your Multiple Sequence Alignment

Recognizing the good parts in a protein alignment

Taking your multiple alignment further

Comparing Sequences That You Cant Align

Making multiple local alignments with the Gibbs sampler

Searching conserved patterns

Internet Resources for Doing Multiple Sequence Comparisons

Making multiple alignments with ClustalW around the clock

Finding your favorite alignment method

Searching for motifs or patterns

Working with Protein 3-D Structures

From Primary to Secondary Structures

Predicting the secondary structure of a protein sequence

Predicting additional structural features

From the Primary Structure to the 3-D Structure

Retrieving and displaying a 3-D structure from a PDB site

Guessing the 3-D structure of your protein

Looking at sequence features in 3-D

Finding proteins with similar shapes

Finding other PDB viewers

Classifying your PDB structure

Doing homology modeling

Folding proteins in a computer


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Threading sequences onto PDB structures

Looking at structures in movement

Predicting interactions

Gene Expression: Microarray Data Analysis

Introduction

Microarray Data Analysis Software and Data Sets

Reproducibility of Microarray Experiments

Microarray Data Analysis: Preprocessing

Scatter Plots and MA Plots

Global and Local Normalization

Accuracy and Precision

Robust Multi-array Analysis (RMA)

Microarray Data Analysis: Inferential Statistics

Expression Ratios

Hypothesis Testing

Corrections for Multiple Comparisons

Significance Analysis of Microarrays (SAM)

From t-Test to ANOVA

Microarray Data Analysis: Descriptive Statistics

Hierarchical Cluster Analysis of Microarray Data

Partitioning Methods for Clustering: k-Means Clustering

Clustering Strategies: Self- Organizing Maps

Principal Components Analysis: Visualizing Microarray Data

Supervised Data Analysis for Classification of Genes or Samples


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Functional Annotation of Microarray Data

Perspective

Pitfalls

Building Phylogenetic Trees

Finding Out What Phylogenetic Trees Can Do for Us

Preparing Your Phylogenetic Data

Choosing the right sequences for the right tree

Preparing your multiple sequence alignment

Building the Kind of Tree we Need

Computing your tree

Knowing whats what in our tree

Displaying your phylogenetic tree

Doing Phylogeny for Free over the Internet

Finding online resources

Finding generic resources

Collections of orthologous genes

Documents

Introduction to Bio