1. The European Bioinformatics Institute (EBI) Toolbox http://www.ebi.ac.uk/Tools/ http://www.ebi.ac.uk/Tools/ Julie Pellegrini Introduction to Bioinformatics

2. What does the Toolbox include? Homology and Similarity Programs Homology and Similarity Programs Protein Functional Analysis Protein Functional Analysis Structural Analysis Structural Analysis Sequence Analysis Sequence Analysis Miscellaneous Tools (clustering, visualization tools for gene expression) Miscellaneous Tools (clustering, visualization tools for gene expression)

3. Homology and Similarity Programs Fasta Fasta Nucleotide, protein, ion channels Nucleotide, protein, ion channels BLAST BLAST Nucleotide, protein, ‘Alternative Splicing’, vectors Nucleotide, protein, ‘Alternative Splicing’, vectors Smith & Waterman Smith & Waterman Protein sequence comparison Protein sequence comparison Databases Databases Proteomes, Genomes, Parasites, SNP Proteomes, Genomes, Parasites, SNP

4. Protein Functional Analysis InterPro InterPro Protein Motif Database InterProScan InterProScan Search InterPro by accession number or sequence Search features Search features Protein repeats, motifs, biochemical function, family

5. Structural Analysis Protein structure analysis and secondary structure prediction Protein structure analysis and secondary structure prediction DALI, MaxSprout Active Site Search Active Site Search NMR elucidation NMR elucidation Protein Quaternary Structure Protein Quaternary Structure PQS, PQS-Quick

6. Sequence Analysis Unknown structure and function can be elucidated through comparison with database of known structures/sequences/functions Unknown structure and function can be elucidated through comparison with database of known structures/sequences/functions ClustalW ClustalW Global Multiple Alignment Global Multiple Alignment EMBOSSALIGN EMBOSSALIGN Like BLAST2 but Global Like BLAST2 but Global Gene finding tools Gene finding tools Translation tools Translation tools Promoter Analysis tools Promoter Analysis tools

7. Miscellaneous Tools BioLayout BioLayout CAST-protein compositional filtering CAST-protein compositional filtering Expression Profiler-gene expression tools Expression Profiler-gene expression tools NEWT NEWT Swiss-Prot Database Swiss-Prot Database Readseq Readseq Converts format Converts format Webservices Webservices Access various biological databases Access various biological databases Protein Colourer Protein Colourer Colors amino acids QuickGo QuickGo Ontology Database search Protein Annotation Assistant Protein Annotation Assistant XEMBL XEMBL EMBL nucleotide sequence data in variety of formats

8. I’ve just discovered a gene! Or have I…? Yeast Genome isolation and sequencing revealed possible protein-coding sequence: ATGTTTACTGGTCAGGAGTATCATTCCGTAGACTCTAATTCCAACAAGCAAAAAGACAACAATAAACGTGGTATTGATGACACATCAAAGAT CTTGAATAATAAGATACCGCACTCTGTTAGTGATACTTCTGCCGCCGCCACCACCACTTCTACTATGAACAATTCTGCTTTAAGTAGATCCT TAGATCCTACTGACATAAACTATAGCACAAATATGGCTGGTGTGGTTGACCAAATACATGATTATACTACTTCCAATAGAAATTCTTTAACCC CACAATATTCTATTGCAGCTGGAAACGTCAATTCGCATGATCGGGTTGTTAAACCCAGCGCCAATTCAAACTATCAGCAGGCTGCATACCTT CGACAACAGCAACAGCAGGATCAGCGACAACAGTCACCCTCTATGAAAACTGAAGAGGAATCCCAACTCTACGGTGATATTCTGATGAAT TCTGGTGTCGTACAGGATATGCATCAGAATCTGGCCACTCATACAAATCTGAGCCAACTGTCGTCTACCCGTAAGTCCGCTCCGAATGATT CTACTACAGCCCCGACTAATGCGTCCAACATCGCCAATACGGCTTCTGTGAACAAGCAGATGTATTTCATGAACATGAATATGAATAACAAC CCACATGCCTTGAACGATCCATCCATCCTGGAAACATTGTCGCCATTTTTTCAACCTTTTGGTGTTGATGTAGCACATTTACCTATGACGAA TCCACCAATTTTCCAAAGTTCTTTGCCTGGATGCGATGAGCCAATTAGAAGAAGAAGAATATCAATCTCTAACGGTCAAATAAGCCAGCTA GGCGAAGATATTGAAACTTTGGAAAACCTGCACAACACACAGCCGCCCCCGATGCCCAATTTTCACAATTATAATGGTCTGAGCCAAACTA GGAATGTATCAAACAAGCCGGTCTTCAACCAAGCAGTGCCGGTTAGTAGTATTCCACAATACAATGCAAAAAAAGTTATTAATCCCACGAA GGACTCCGCATTGGGTGATCAGAGCGTTATTTACTCGAAAAGTCAGCAGCGAAATTTTGTAAACGCGCCATCAAAGAATACTCCAGCGGA GAGTATAAGTGATTTGGAAGGCATGACGACGTTTGCGCCAACTACTGGAGGTGAAAATAGGGGCAAATCTGCACTTAGGGAATCTCACTC TAATCCTAGCTTCACTCCAAAATCTCAAGGATCTCATTTAAATTTAGCGGCGAACACACAGGGAAATCCAATCCCTGGTACTACGGCATGG AAGAGAGCAAGATTGTTAGAAAGAAATCGAATTGCAGCTTCGAAATGTAGACAAAGGAAAAAGGTTGCGCAGCTGCAGCTCCAAAAGGAA TTTAACGAAATTAAAGACGAGAATAGAATTTTACTGAAAAAGTTAAATTACTATGAAAAACTAATCTCTAAATTCAAGAAATTCTCCAAAATT CATTTACGTGAACATGAAAAACTAAATAAAGACTCAGATAATAATGTTAATGGCACTAATAGTAGCAACAAAAATGAAAGCATGACTGTGGA TTCATTAAAGATCATTGAAGAACTTTTAATGATCGATTCAGACGTTACAGAAGTGGATAAAGATACTGGTAAGATCATAGCCATCAAGCACG AGCCATACTCTCAACGTTTCGGAAGCGATACTGACGATGACGATATAGATCTCAAGCCCGTAGAAGGTGGTAAGGATCCAGACAACCAAT CATTACCCAATTCTGAAAAGATAAAATAA

9. What sorts of protein does my newly discovered gene code for?? Paste discovered gene into Transeq to find protein sequence Paste discovered gene into Transeq to find protein sequence

10. Use PPSearch on the TranSeq Output

11. How does our protein sequence compare with known cross- references? Here is a Case for Sequence Alignments! Here is a Case for Sequence Alignments! Use Align, ClustalW… Use Align, ClustalW… Method Gap Open Gap Open Gap Extend Gap Extend Molecule Matrix

12. Align Output Findings We have in fact found what our gene codes for (YCA2) and it has already been added to the protein database.