<p>Introductory molecular biology computing and bioinformatics</p><p> for Molecular Mechanisms of Development. </p><p>Barcelona 2006.</p><p>Exercise Set 1 </p><p>1. Find the protein amino acid sequence of the mouse haematopoietic cell </p><p> protein kinase called “tec” described by Mano et al. in 1993. Create a text </p><p> file (.txt) containing this sequence in FASTA format.</p><p>2. Find the sequence of the protein with accession number AAA37592. </p><p>Create a text file (.txt) containing this sequence in FASTA format. </p><p>3. Find the complimentary DNA (cDNA) sequence with accession number </p><p>BC018394. Translate this nucleotide sequence into the corresponding </p><p> protein amino acid sequence and save this file. Edit the protein sequence </p><p> into FASTA format and save it as a text file (.txt)</p><p>4. Perform a BLAST search with the tec kinase sequence you have saved. </p><p>Make notes on any conserved domains that are expected to be present in </p><p> the protein. Format your output before proceeding.</p><p>5. Examine the “E values” or “Expect scores”. What have these scores been </p><p> used to do to your list of BLAST hits? Can you follow a link from the </p><p>BLAST page to notes on what this score means?</p><p>6. From the BLAST search output find the protein sequence for Bruton </p><p> agammaglobulinemia / Bruton’s tyrosine kinase….. submitted by Tsukada</p><p> et al. in 1993. Create a text file (.txt) containing this sequence in FASTA </p><p> format. 7. From the BLAST search find the protein sequence for mouse BMX non-</p><p> receptor tyrosine kinase submitted by Ekman et al. in 1997. Create a text </p><p> file (.txt) containing this sequence in FASTA format.</p><p>8. Create a single text file (.txt) containing all of your saved protein </p><p> sequences. Edit the top identifier line (everything to the RHS of the > </p><p> symbol) so that each sequence is identified by a single short name, each </p><p> one beginning with either a different letter or number. Eliminate any blank </p><p> lines to remove spaces between the blocks of to describe each sequence.</p><p>9. Use this file containing all of your sequences to obtain a multiple sequence</p><p> alignment (MSA) and save the alignment. You should use either ClustalW</p><p> or Multalin.</p><p>Please note the following points if you use ClustalW/Boxshade, </p><p> a) set the ClustalW output format to wo/numbers,</p><p> b) follow the link to obtain the output file in .aln format (alignment file) and</p><p> copy the resulting page </p><p> c) paste the .aln output into the Boxshade window and set output to </p><p> either rtf new or rtf old and input to ALN. </p><p>10.Use PFAM and InterPro (and any other programmes from the “Analysing </p><p> sequences” section of the tool box) to analyse your tec kinase protein </p><p> sequence. Determine which, if any, domains are common to all of </p><p> sequences present in your MSA. Annotate your alignment to highlight this </p><p> region of similarity.</p><p>Geraint Thomas Department of Physiology, UCL 2006 </p>