Lecture 1

general

• "Pera Poogibo"
• theoretical: inside the bioinformatics black box... overview of methods
• applied bioinformatics
• NCBI - evolutionary genomics research group
• Pere, David, Ben, Yoo-Ah Sijung
• 4 projects - deadline is day of journal club
• ben.busby@gmail.com - use this
  • applied bioinformatics class in library
  • two scripting courses - perl python
  • medical genomics course
  • theoretical genomics
  • database design

bioinformatics

• wet fishing expeditions are costly
• pub med literature searches
  • boolean operators AND OR
  • "search phrase"
  • wildcard oxida*
  • fields [bracket delimited]

dna sequencing information

• NCBI - Gene db with information about molecule
  • key field restrictions: organism, gene, (official symbol of gene locus), chromosome, title, accession
  • unique id for each molecule
• NCBI - Nucleotide - RNA sequence
• Joint genome institute DOE
• ensembl
  • ENST
  • waning in popularity these days
• UCSC genome browser
• Galaxy
  • short read - alumina read
  • tools like bowtie (compilation required)
  • 200GB - good for one project
• DAVID
• Extremobase
• model organisms like drsophila and c elegans

rna sequence

• microRNAs
  • miRBase
• regulatory information
  • transfac
• trace/SRA
  • RNAseq
  • best to load up into GALAXY
• ncRNA - non-coding RNA
• CoreNucleotide (genBank)
  • key fields: organism accession, author, title sequence length properties gene
  • VOCAB - seed sequence

RNA expression (microarray)

• NCBI- GEO
  • GDS entries better than GSE datasets
• Stanford Microarray database
• UCSC precomputed normalization
• tissue-specific microarray data
  • bioGPS

SNPs

• 1000 genome project - 10 GB
• dbSNP

comparative genomics

• taxonomic and chromosomal information
• NCBI
  • taxonomy
  • genome
  • cancer chromosome

proteins

• NCBI - Protein - largest db in world
  • key field restrictions: organism, title, author, mol wt, seq length, gene, [ecno] enzyme commission number
  • ec number categorize
  • example: cps1 AND homosapiens
  • go to gene page
  • HOT: alternate reading frames nested genes
• VOCAB - protein domain - chunk of protein that is conserved btw species
  • CDD, SMART, PFAM
  • compare orthology
• structural info
  • RCSB protein data bank (pdb)
  • use to grab protein structures
• binding information
  • string - problem no so accurate - uses text mining
  • go to protein - what bind to? cog? networks?
  • text-mining - watson
  • ex:
    • two proteins - LAMP1 GANKYRIN
• network and functional info
  • KEGG -- HIGH RECOMMENDATION BY BEN BUSBY!
  • kyoto encyclopedia of genes and genomes
  • shows pathways
  • KEGG pathway database
    • enter keywords argenine biosynthesis
    • making pics for presentations

phosphorylation

• proleins
• kinase - catalyze
• phosphorylase - takes off
• COOL - titin

intron structure

• NCBI - nucleotide
  • search for word join - find intronic coordinated - gives offset

homology vs similarity

• cannot say somewhat homologous
  • a quantitative statement describing
• can say somewhat similar
• identity - when aligned, x# of nucleotides are the same
• 70% identical on amino acid level = 97% chance of having same structure
  • for function purposes probably doing more or less the same thing

evolution in 15 minutes

• COOL: pseudomonas natriegens
• microevolution - changes in gene frequency in pop from one generation to the next
• macroevolution - descent of different species from a common ancestor over many generations - accumulation of variation
• nothing in biology makes sense except in light of evolution - dobzhansky, 1973
• requires descendent through genetic inheritance
• the first phylogenetic tree - from darwin notebook in 1837 ("I think")
• origin of species 1859 - only one picture!
• model of speciation - separated populations
• fitch WM 2000 Homology
• homologous features vs analogous features
• Molecules as documents - beginning of
• homology in molecular data
• gene duplication, orthologues and paralogues
  • paralogues - process of duplication
  • orthologues - speciation
• horizontal gene transfer
  • transformation, transduction, bacterial conjugation - Dolittle 1996

5 steps of phylogenomics dancing

1. sequence data
2. align sequence
3. phylogenetic signal? patterns-> evolutionary processes?
4. characters based methods vs distance methods
5. calculate best fit tree
6. bootstrap - test phylogenetic reliability

• gene tree don't necessarily give us species tree

more ben

• entrez - manually curated db
• genBank and RefSeq - GI (GenBank Identifier)
• e-utilities
  • E-fetch
  • put in a wait command, batches of 50 and three second
• NCBI ftp site
  • aspericyte
  • genbank sequence data files ncbi-asn1