Bioinformatics Primer

1
Bioinformatics Primer

• Goal Introductory skills for bioinformatics
  analysis.
• Format Complete the exercises, ask anything.

2
Basic Skills interpro

• interpro (www.ebi.ac.uk/interpro/)?
• Exercise
• for 3 proteins important to your research area
  (choose 2 well defined, 1 not well defined)?
• download their protein sequence
  fromwww.ncbi.nlm.nih.gov
• analyse them using interpro
• what domains do they contain?
• what are the functions of these domains?
• what families do the proteins belong to?
• how would you do this on 100 proteins, or 20,000
  proteins?

3
Basic Skills gene ontologies

• Gene Ontology database
• www.geneontology.org?
• Exercise
• Keep this information saved as you will use it
  thje following days
• 1) Define
• Molecular function
• Biological process
• Subcellular location
• 2) Find GO identifiers that describe functions,
  processes or locations that are relevant to your
  research
• List the identifier, type and description.
• Should you use identifiers further up or down the
  hierarchy?

4
Basic Skills gene ontologies

• Exercise continued
• 3) For 3 proteins relevant to your research
• What GO terms are assigned to the protein?
• What evidence is there for the assignments?
• 4) Describe the difference between the evidence
  codes.
• 5) How would you find all proteins with a
  specific molecular function?

5
Basic Skills ArrayExpress/GEO

• GEO/ArrayExpress
• Microarray repository tools containing published
  microarray data
• Note differences in ease of use and completeness!
• Exercise
• Compare GEO and ArrayExpress.
• Search for Human stem cell microarray studies
• What are the GEO/ArrayExpress identifiers for
  some recent Stem cell microarray studies?
• What data is available? Raw data? Processed data?
• Download a CEL file (or set of CEL files) from a
  stem cell microarray study.
• Go to ArrayExpress Atlas
• Look up at least two genes of interest (in stem
  cell biology)?
• What does the database tell you?

6
Basic Skills Ensembl

• Exercise
• Go to Ensembl. Describe it.
• Look up a (human) gene. How many transcript
  variants does it have?
• Explore!
• Use BioMart to gather all Ensembl identifiers and
  Entrez geneIDs for all human and mouse genes,
  export this data into excel (you will need this
  later).

7
Basic Skills UCSC

• Exercise
• Go to genome.ucsc.edu.
• Look up a (human) gene. Select many different
  gene models how many transcript variants are
  found for your gene in UCSC known genes, AceView,
  Refseq?
• Use the table browser to download all human genes
  (refseq) into excel.
• What else of interest can you download?

8
Basic Skills R

• See accompanying worksheet

9
Basic Skills command line login

• Try this on your own laptop
• Windows command line
• windowsR, type cmd
• Cygwin (unix in windows)?
• open cygwin
• putty (log into a unix server)?
• ip address, username, password
• VMware (virtual machine within windows)?
• choose a unix virtual machine (i.e. tinyunix)?
• open a terminal
• Apple Mac
• OS X open a terminal

10
Basic Skills command line

• Basic command line operations
• Directories
• cd ltdirectorygt Change the current directory
• pwd get current working directory
• Viewing files and directories
• ls ltpathgt list the contents of a directory
  (dir)?
• more ltfilegt see contents of file on screen,
  stop after every page
• less ltfilegt see contents of file (with better
  ability to move in the file)?
• cat ltfilegt see contents of file, don't stop at
  new page

11
Basic Skills command line

• Basic command line operations
• Editing files
• emacs ltfilegt open file for editing in emacs
• other programs nedit, vi
• Copying and moving files
• cp ltfilegt ltdestinationgt copy file to
  destination (copy)?
• mv ltfilegt ltdestinationgt move (or rename) file
  to destination (move)?

12
Basic Skills command line

• Basic command line operations
• login and copying
• ssh / scp login to server, copy files
• viewing parts of files
• head -lines ltfilegt look at first lines
• tail -lines ltfilegt look at last lines
• pattern matching
• grep -e patternltfilegt find lines in file with
  pattern
• grep -v patternltfilegt find lines in file
  without pattern
• counting
• wc ltfilegt count words, lines in file

13
Basic Skills command line

• Basic command line operations
• gt ltfilegt send results to file
• more filename gt filename2 (send all of filename
  to filename2)?
• ls gt directory_contents.txt
• pipe send the results forward to another
  program
• grep -e pattern filename gt filename_pattern.txt
• head -5 filename gt filename_pattern.txt

14
command line exercises

• Create a directory, name it after yourself
• What is the current working directory?
• Copy exercise.txt into your directory
• Change the working directory to that directory
• Look at the file with more
• Read the man page for wc with man wc
• What are the first 5 lines?
• What are the last 3 lines?
• How many lines contain the word fish? (hint you
  need to use pipe)?

15
command line exercises

• command line in windows
• Test the following in windows command line (open
  with windows-key R, then cmd)?
• more
• (pipe)?
• grep
• wc
• sed
• Which work, which do not?
• How do you find help for a program??
• What is sed for?

16
Additional resources

• Plenty of tutorials are available online for R
  and unix
• Unix tutorial for beginers
• http//www.ee.surrey.ac.uk/Teaching/Unix/
• R
• http//cran.r-project.org/other-docs.html
• Note some are very large (100 pages)?