Bioinformatics

Coined by Paulien Hogeweg in 1979 for the study of informatics processes in biotic systems

Bioinformatics

Computer databases

1. medicine - understand life processes in health / disease states 2. genetic disease databases 3. genetic maps - to identify genes for heritable traits and unravel patterns of genome organization 4. comparisons of genome sequences - between different organisms can help to clarify evolutionary relationships 5. forensics 6. designing primers for DNA amplification (PCR) 7. provides a complete list of candidate genes for drug discovery 8. pharma companies - search for better/new drugs 9. agriculture - develop disease and drought resistant plants and develop higher yield crops

Genetic disease (SNP) databases

To store information (DNA profiles) of convicted offenders making their identification easier in subsequent crimes (CODIS) - combined DNA index system

1. simple sequence analysis 2. gene finding 3. regulatory regions 4. whole genome annotations 5. comparative genomics

1. spice variants 2. tissue specific expression 3. structure 4. single gene analysis (cloning techniques) 5. experimental data w/ thousands of genes simultaneously 6. DNA chips, micro-arrays and expression array analysis

1. Homology (protein families) 2. conserved domains/regions 3. structure determination (molecular modeling) - 2D, 3D, quaternary 4. protein function 5. analysis often involved 2D gels and mass spectometry

1. GenBank - National center for biotech info (NIH genetic sequence database part of the international nucleotide sequence database collab) 2. EMBL - european molec bio lab - euro equivalent to US gen bank 3. DNA data bank of Japan - Japan's national institute of genetics, 3rd in trio of major nucleotide sequence databases

1. UniProt - United protein database 2. PIR - protein information resource database 3. Swiss-prot 4. ExPASY - expert protein analysis system

Query sequence

15 nucleotides or amino acids

FASTA bare sequence identifier (accession number or gene info ID)

Alignment

Basic Local Alignment Search Tool widely used software in bioinformatics research main function - to compare a sequence of interest, the query sequence, to sequences in a large database

Score value **the higher the score the better the alignment**

E-value (expectation value) **the lower the e-value the better the match**

genome annotation

GOAL - to create a labeled genome, where biological information is linked to sequence Structural and Functional annotations

Structural annotation

ORFs and their localization gene structure coding regions location of regulatory motifs

biochemical function biological function involved regulation and interactions expression

Using BLAST for finding similarities and then annotating genomes based on that

functional annotation

A list of all the genes identified and the proteins and enzymes that are encoded by them - activities of this set of proteins (REGULATION) accounts for the cell structure and behavior on its environment

It can be explored by clicking and sliding - info about every gene and possible genes that are available - arrows represent genes that can be selected

1. To identify genes within a long DNA sequence 2. DNA sequence that codes for amino acids should not contain any stop codons 3. each DNA strand can be read in 3 reading frames - there are 2 DNA strands 4. computer must analyze a given DNA sequence in 6 different reading frames (3x2) = 6

open reading frame

Open reading frame finding (ORF finder) at NCBI and GENSCAN

Open Reading Frame (ORF) Start codon (met - ATG) Stop codon (TGA, TAG, TAA) Terminator sequence (Prok) Shine Delgano (Prok) TATA box (Euk) Kozak sequence (Euk) Poly A addition signal (Euk) Intron/exon boundaries CpG islands

Effective for the analysis of bacteria DNA genomic sequences NOT effective for analyzing the DNA for eukaryotes

the Intron/exon structure - a more sophisticated gene identification software is required for euks

Ab Initio they attempt to predict genes based only on the knowledge and understanding gene structure

1. Should begin with a start codon (met) 2. must be of reasonable size (longer the better) 3. Must end with an in-frame stop codon

Long ORFs are unlikely to occur by chance and thus signify potential genes - short AAs sequences are prob not ORFs many stop codons close together suggest and ORF is not present

Computer analysis - Sequence alignment software

BLAST - basic local alignment search tool FASTA - FAST ALL

BLAST

1 - look for similar segments *high-scoring segment pair (HSPs) between query sequence and database sequence 2 - evaluate statistical significance of any matches that were found 3 - report only those matches that satisfy a user-selectable threshold of significance

To find regions of sequence similarity

The structure and function of this novel sequence and its evolutionary history and homology with other sequences in the database

local - where the region of similarity is based in 1 location or global - where regions of similarity can be detected across otherwise unrelated genetic code

BLAST N

BLAST P

BLAST X - compares the 6 frame translations of DNA query to protein databases

tblastn

tblastx - compares the 6 frame translations of DNA query to 6-frame translations of a DNA database (each sequence is comparable to BLASTP searches!)

FASTA

FASTX

TFASTA

FASTA Bare sequence Identifiers

FASTA - recommended that all lines of text be shorter than 80 characters in length - blank lines not allowed in the middle - sequences are expected to be represented in the standard IUB/IUPAC amino acid & nucleic acid codes - single hyphen or dash can be used to rep gap of indeterminate length

Bare sequence - ex - Gen bank / gen pept flatfile report - BLANKE LINES NOT ALLOWED

Identifiers

specific syntax may consist of only one token (WORD) spaces between letters will cause it to be a bare sequence - spaces before/after identifier are not allowed

Sequence Homology

more similar to each other than if they are more distantly related

family trees of organisms

Bacteria from different species can exchange DNA sequences (horizontal transfer)

CLUSTAL W and COBALT (constrained-baed multiple alignment tool)

Phylogenetic tree (or evolutionary tree)

Based upon similarities and differences in the species' physical and/or genetic characteristics implies that the taxa joined together in the tree (nodes) have descended from a common ancestor

ancestor - tree trunk organisms that have arisen from the ancestor - at the tips of tree branches *closely related groups are located on branches close to one another

NCBI *all for the better understanding of molec processes affecting human health and disease

MASCOT search engine from matrix science

Peptide fingerprint Sequence Query MS/MS ion search Nucleic or amino acid database in FASTA format

Biological redundancy and multiplicity - different sequences w/ similar structures -organisms with similar genes -multiple functions of single genes -grouping of genes in pathways sequence redundancy in genomes significance of relationships & similarities signal vs. noise (you want signal not noise) lack of data

bioinformatics laboratory *practices query, retrieval and analysis of sequences*