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Introduction to Bioinformatics

Introduction to Bioinformatics. Lisa Mullan, HGMP-RC. What is it?. Bioinformaticians -. Develop bioinformatics tools (software). Bioinformatics users -. Use bioinformatics tools. What are these tools?. Similarity searching. Primer design. Nucleic acid translation. Sequence alignment.

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Introduction to Bioinformatics

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  1. Introduction to Bioinformatics Lisa Mullan, HGMP-RC

  2. What is it? Bioinformaticians - Develop bioinformatics tools (software) Bioinformatics users - Use bioinformatics tools

  3. What are these tools? Similarity searching Primer design Nucleic acid translation Sequence alignment Pattern finding Gene prediction Structure prediction

  4. Where do I find them? http://www.ebi.ac.uk http://www.sanger.ac.uk http://www.hgmp.mrc.ac.uk http://www.ncbi.nlm.nih.gov http://www.expasy.ch http://pbil.univ-lyon.fr On the web Or you can download packages of programs onto your own computers

  5. Searching for a sequence Entrez http://ww.ncbi.nlm.nih.gov/Entrez SRS Most sites use a “sequence search engine”

  6. FASTA Format >Sequence description MNEGDTHYYNKLPPDSEFGDNHVVILCNMFFHRTEYWWDFCDVNMVCDHGGSAEQQR Text (plain) Format MNEGDTHYYNKLPPDSEFGDNHVVILCNMFFHRTEYWWDFCDVNMVCDHGGSAEQQR What does it look like?

  7. Save it as a txt file - Notepad, Teachtext, ASCII format Cut and paste into web based tools - BLAST, PeptideMass Input for programs as part of a larger package - EMBOSS, GCG and what do I do with it?

  8. Human Genome Mapping Project – Resource Centre Funded by the Medical Research Council Provide biological and bioinformatics support to the academic community Software development and biological research

  9. A word about X DOS MacOS UNIX Personal Computers Apple Macintosh Workstations X translates “unix-speak” into DOS and MacOS http://www.hgmp.mrc.ac.uk/Registered/Webapp/vnc/

  10. (root) people/ data/ mrna41/ mrna01/ lmullan/ Basic UNIX commands cp – copy ls – list (directory contents) seq.fasta mv – move or rename rm – delete (remove) cd – change directory pwd – print working directory mkdir – make a directory rmdir – remove (delete) a directory

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