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The European Bioinformatics Institute (EBI) Toolbox ebi.ac.uk/Tools/

The European Bioinformatics Institute (EBI) Toolbox http://www.ebi.ac.uk/Tools/. Julie Pellegrini Introduction to Bioinformatics. What does the Toolbox include?. Homology and Similarity Programs Protein Functional Analysis Structural Analysis Sequence Analysis

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The European Bioinformatics Institute (EBI) Toolbox ebi.ac.uk/Tools/

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

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

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

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

  5. Structural Analysis • Protein structure analysis and secondary structure prediction • DALI, MaxSprout • Active Site Search • NMR elucidation • 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 • ClustalW • Global Multiple Alignment • EMBOSSALIGN • Like BLAST2 but Global • Gene finding tools • Translation tools • Promoter Analysis tools

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

  8. I’ve just discovered a gene! Or have I…? YeastGenome isolation and sequencing revealed possible protein-coding sequence: ATGTTTACTGGTCAGGAGTATCATTCCGTAGACTCTAATTCCAACAAGCAAAAAGACAACAATAAACGTGGTATTGATGACACATCAAAGATCTTGAATAATAAGATACCGCACTCTGTTAGTGATACTTCTGCCGCCGCCACCACCACTTCTACTATGAACAATTCTGCTTTAAGTAGATCCTTAGATCCTACTGACATAAACTATAGCACAAATATGGCTGGTGTGGTTGACCAAATACATGATTATACTACTTCCAATAGAAATTCTTTAACCCCACAATATTCTATTGCAGCTGGAAACGTCAATTCGCATGATCGGGTTGTTAAACCCAGCGCCAATTCAAACTATCAGCAGGCTGCATACCTTCGACAACAGCAACAGCAGGATCAGCGACAACAGTCACCCTCTATGAAAACTGAAGAGGAATCCCAACTCTACGGTGATATTCTGATGAATTCTGGTGTCGTACAGGATATGCATCAGAATCTGGCCACTCATACAAATCTGAGCCAACTGTCGTCTACCCGTAAGTCCGCTCCGAATGATTCTACTACAGCCCCGACTAATGCGTCCAACATCGCCAATACGGCTTCTGTGAACAAGCAGATGTATTTCATGAACATGAATATGAATAACAACCCACATGCCTTGAACGATCCATCCATCCTGGAAACATTGTCGCCATTTTTTCAACCTTTTGGTGTTGATGTAGCACATTTACCTATGACGAATCCACCAATTTTCCAAAGTTCTTTGCCTGGATGCGATGAGCCAATTAGAAGAAGAAGAATATCAATCTCTAACGGTCAAATAAGCCAGCTAGGCGAAGATATTGAAACTTTGGAAAACCTGCACAACACACAGCCGCCCCCGATGCCCAATTTTCACAATTATAATGGTCTGAGCCAAACTAGGAATGTATCAAACAAGCCGGTCTTCAACCAAGCAGTGCCGGTTAGTAGTATTCCACAATACAATGCAAAAAAAGTTATTAATCCCACGAAGGACTCCGCATTGGGTGATCAGAGCGTTATTTACTCGAAAAGTCAGCAGCGAAATTTTGTAAACGCGCCATCAAAGAATACTCCAGCGGAGAGTATAAGTGATTTGGAAGGCATGACGACGTTTGCGCCAACTACTGGAGGTGAAAATAGGGGCAAATCTGCACTTAGGGAATCTCACTCTAATCCTAGCTTCACTCCAAAATCTCAAGGATCTCATTTAAATTTAGCGGCGAACACACAGGGAAATCCAATCCCTGGTACTACGGCATGGAAGAGAGCAAGATTGTTAGAAAGAAATCGAATTGCAGCTTCGAAATGTAGACAAAGGAAAAAGGTTGCGCAGCTGCAGCTCCAAAAGGAATTTAACGAAATTAAAGACGAGAATAGAATTTTACTGAAAAAGTTAAATTACTATGAAAAACTAATCTCTAAATTCAAGAAATTCTCCAAAATTCATTTACGTGAACATGAAAAACTAAATAAAGACTCAGATAATAATGTTAATGGCACTAATAGTAGCAACAAAAATGAAAGCATGACTGTGGATTCATTAAAGATCATTGAAGAACTTTTAATGATCGATTCAGACGTTACAGAAGTGGATAAAGATACTGGTAAGATCATAGCCATCAAGCACGAGCCATACTCTCAACGTTTCGGAAGCGATACTGACGATGACGATATAGATCTCAAGCCCGTAGAAGGTGGTAAGGATCCAGACAACCAATCATTACCCAATTCTGAAAAGATAAAATAA

  9. What sorts of protein does my newly discovered gene code for?? • 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! • Use Align, ClustalW…

  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.

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