Introduction to Bioinformatics CPSC 265

Interface of biology and computer science Analysis of proteins, genes and genomes using computer algorithms and computer databases Genome informatics: making sense of the billions of base pairs of DNA that are sequenced by genomics projects. Mostly, it’s about protein and DNA sequences What is bioinformatics?

What do bioinformatics researchers do? Process large data outputs from new technologies Turn sequence data into whole-genome sequences Interpret genome sequences in terms of genes and their expression Find genes that control crop, animal traits, disease etc. Model evolution in genomes and proteins Model and predict 3D structures of proteins

Growth of GenBank Year Base pairs of DNA (billions) Sequences (millions) Updated : >40b base pairs Fig. 2.1 Page 17

Cost of sequencing is falling exponentially

DNA sequence analysis Could be like those from our experiment last week Or, a lot bigger, like the whole human genome. Some have chromatogram or “quality” data, some don’t.

DNA makes RNA makes protein Hard to sequence RNA Very hard to sequence protein We can deduce RNA sequence from DNA (in bacteria, as easy as turning Ts to Us. In eukarya, need also to figure out where introns are) We can deduce protein sequence from RNA, using the Universal Genetic Code

Conceptual Translation In a computer, take each set of three RNA letters, and then figure out what amino acid they code for. Professional biologists use the SINGLE LETTER CODE

DNA potentially encodes six proteins 5’ CAT CAA 5’ ATC AAC 5’ TCA ACT 5’ GTG GGT 5’ TGG GTA 5’ GGG TAG 5’ CATCAACTACAACTCCAAAGACACCCTTACACATCAACAAACCTACCCAC 3’ 3’ GTAGTTGATGTTGAGGTTTCTGTGGGAATGTGTAGTTGTTTGGATGGGTG 5’

We call these READING FRAMES 5’ CAT CAA 5’ ATC AAT 5’ TCA ATG 5’ GTG GGT 5’ TGG GTA 5’ GGG TAG 5’ CATCAATGACAACTCCAAAGACACCCTTACACATCAACAAACCTACCCAC 3’ 3’ GTAGTTACTGTTGAGGTTTCTGTGGGAATGTGTAGTTGTTTGGATGGGTG 5’

All proteins start with M (ATG) TAG, TAA and TGA are all STOP This can help narrow it down 5’ CAT CAA 5’ ATC AAT 5’ TCA ATG 5’ GTG GGT 5’ TGG GTA 5’ GGG TAG 5’ CATCAATGACAACTCCAAAGACACCCTTACACATCAACAAACCTACCCAC 3’ 3’ GTAGTTACTGTTGAGGTTTCTGTGGGAATGTGTAGTTGTTTGGATGGGTG 5’

Once you know the sequence of the protein, you can figure out if it has been studied already. You may even be able to track down a likely structure

GenBankEMBLDDBJ Housed at EBI European Bioinformatics Institute There are three major public DNA databases Housed at NCBI National Center for Biotechnology Information Housed in Japan Page 16

PubMed is… National Library of Medicine's search service 12 million citations in MEDLINE links to participating online journals PubMed tutorial (via “Education” on side bar)

BLAST is… Basic Local Alignment Search Tool NCBI's sequence similarity search tool supports analysis of DNA and protein databases 80,000 searches per day

TaxBrowser is… browser for the major divisions of living organisms (archaea, bacteria, eukaryota, viruses) taxonomy information such as genetic codes molecular data on extinct organisms

From the NCBI home page, type “lectin” and hit “Search”

PubMed is the NCBI gateway to MEDLINE. MEDLINE contains bibliographic citations and author abstracts from over 4,600 journals published in the United States and in 70 foreign countries. It has 12 million records dating back to Page 35 PubMed

BLAST BLAST looks for similarity between your favorite query sequence and other known protein or DNA sequences. Applications include identifying homologs (orthologs and paralogs) discovering new genes or proteins discovering variants of genes or proteins investigating expressed sequence tags (ESTs) exploring protein structure and function page 88

Four components to a BLAST search (1) Obtain the sequence (query) (2) Select the BLAST program (3) Enter sequence (4) Choose optional parameters Then click “BLAST” page 88

Step 2: Choose the BLAST program blastn (nucleotide BLAST) blastp (protein BLAST) tblastn (translated BLAST) blastx (translated BLAST) tblastx (translated BLAST)

DNA potentially encodes six proteins 5’ CAT CAA 5’ ATC AAC 5’ TCA ACT 5’ GTG GGT 5’ TGG GTA 5’ GGG TAG 5’ CATCAACTACAACTCCAAAGACACCCTTACACATCAACAAACCTACCCAC 3’ 3’ GTAGTTGATGTTGAGGTTTCTGTGGGAATGTGTAGTTGTTTGGATGGGTG 5’

Choose the BLAST program ProgramInputDatabase 1 blastnDNADNA 1 blastpproteinprotein 6 blastxDNAprotein 6 tblastnprotein DNA 36 tblastxDNA DNA

Step 3: choose the database nr = non-redundant protein (most general database) Also can search specific organisms and DNA rather than protein (although ALL DNA is going to take a long time…)

filtering

So now you can Find any sequence in the database Find relevant publications Match DNA to protein sequence Find database matches to DNA or protein Find conserved domains in protein Find the 3D structure of a protein …Without doing any experiments!