July LJM Introduction to Bioinformatics Lisa Mullan, HGMP-RC

July LJM Bioinformaticians - Develop bioinformatics tools (software) Bioinformatics users - Use bioinformatics tools

July LJM Structure prediction Primer design Sequence alignment Similarity searching Pattern finding Nucleic acid translation Gene prediction

July LJM On the web Or you can download packages of programs onto your own computers

July LJM Most sites use a “sequence search engine” Entrez SRS

July LJM Text (plain) Format MNEGDTHYYNKLPPDSEFGDNHVVILCNM FFHRTEYWWDFCDVNMVCDHGGSAEQQR FASTA Format MNEGDTHYYNKLPPDSEFGDNHVVILCNM FFHRTEYWWDFCDVNMVCDHGGSAEQQR >Sequence description

July LJM 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

July LJM 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

July LJM DOSMacOSUNIX Personal ComputersApple MacintoshWorkstations X translates “unix-speak” into DOS and MacOS

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