Introduction to Bioinformatics

Lecturer: Dr. Yael Mandel-Gutfreund

Teaching Assistant: Shula Shazman Sivan Bercovici

Course web site :http://webcourse.cs.technion.ac.il/236523

Course Structure and Requirements

1.Class Structure1. 2 hours Lecture 2. 1 hour tutorial

2. Home work• Homework projects will be given every third week• The homework will be done in pairs.• 4/4 homework projects submitted

2.A final project will be conducted and submitted in pairs

Grading

• 30% Homework assignments• 70% final project

Bioinformatics

• An approach to mine knowledge from biological data.

• A bunch of methods to ease biological research in the lab.

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Biological Databases

Tutorial 1

http://www.ncbi.nlm.nih.gov/

http://www.genome.ucsc.edu/

o DNA,RNA & Protein sequences

o RNA & Prot. Structure

o Gene Expression

o Protein localization

o Mutations

o Similarity between species

o Specie Specific database

o Literature

o Experimental support

Biological Sequences: RefSeq

A comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products.

• Genomic Sequences.• known mRNAs.• Predicted mRNAs:

- Putative genes (homologue to known gene).- Orphan genes (look like ORFs but have no homologues).

• Known Proteins.• Predicted Proteins (Putative & Orphan).

RefSeq

Comprehensive, it covers a wide variety of sequences.

• Complete genomic molecules.

•Incomplete genomic regions.

•Transcript products.

•Protein products.

•Non-coding transcripts.

• Predicted Transcript products.

• Predicted Protein products.

How to identify each kind of sequence?: accession numbers.

RefSeqAccession Number: A unique identifier given to a sequence

ExampleKind of sequence

Description

NC_123456DNAComplete genomic molecules (genomes, chromosomes, organelles, plasmids).

AC_123456DNAAlternative Genomic Assembly.

NT_123456DNAIncomplete Genomic Assembly

NG_123456DNAIncomplete genomic regions.

NM_123456RNATranscript products; Mature mRNA protein-coding transcripts.

NP_123456ProteinProtein products; full-length products & partial proteins.

NR_123456RNANon-coding transcripts including tRNAs, rRNAs and others.

XM_123456RNAPredicted Transcript products; model mRNA corresponding to the genomic contigs.

XP_123456ProteinPredicted Protein products; model proteins corresponds to the genomic contigs.

Complete Table:http://www.ncbi.nlm.nih.gov/RefSeq/key.html

ENTREZ

Integrated, It is related to other databases through ENTREZ,A NCBI interface that connects between different Databases.

RefSeq

PubMed(Literature)

GEO(Gene

Expression)

PDB(Protein Structure)Uni-Prot

)Protein Sequences(

GenBank)genomic

data(

OMIM)genetic

disorders(

ENTREZ: http://www.ncbi.nlm.nih.gov/Entrez/

LiteratureSequences Disease

Gene ExpressionProt. StructureSimilarity between species

Experimental support

Integrated databaseEntrez

RefSeq is non-redundant, each sequence is represented only once.

But...What is redundancy in biological databases?

Are two alleles of the same locus redundant?Are the same loci in two closely related organisms redundant? Are two gene copies redundant?

It depends on the kind of database.

In RefSeq two alleles from a same locus are considered redundant.In RefSeq two loci from closely related organisms are not redundat.In RefSeq two gene copies are not redundant.

At last…

• A Bioinformatic Navigator that concentrates information

from various sources.• It enables visualization of a big amount of information at the

same time.

Genome Browser

cftr

Chromosome Coordinates

Chromosome Position

mRNAs

EvolutionaryConservation

5 ’UTR ORF…

Display optionsFull>Pack>Squish>Dense>Hide