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Function preserves sequences

Christophe Roos - MediCel ltd christophe.roos@ medicel .fi. Function preserves sequences. Mutations change sequences. Molecular evolution. Part 3: sequence databases & comparisons. Similarity is the result of conservation or converging evolution – it has its reason of being.

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Function preserves sequences

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  1. Christophe Roos - MediCel ltd christophe.roos@medicel.fi Function preserves sequences Mutations change sequences Molecular evolution Part 3: sequence databases & comparisons Similarity is the result of conservation or converging evolution – it has its reason of being

  2. The public biological databases • EMBL or GenBank or DDBJ for DNA • emblnew for daily updates, merges the main DB 4x/year • SwissProt or PIR for proteins • Trembl, tremblnew, remtrembl • PDB for structures • In flat file format, yet quite informative and convertible • Fasta format is a ‘universal’ sequence format: first line starts with ‘>’ followed by free text. Second line has the start of the sequence (50 or 60 characters per line). Use the first line for the name or the Accession Number (AC) Christophe Roos - 3/6 Sequence databases & comparison

  3. Database homes • The European database home is in Hinxton, Cambridge, UK: European Bioinformatics Institute - EBI • http://www.ebi.ac.uk • Access through the Sequence Retrieval System, SRS • The American database home is in Washington DC: National Center for Biotechnology Information – NCBI • http://www.ncbi.nlm.nih.gov • Access through Entrez • Both centers exchange their data on a daily basis, however there are differences in annotations, consistency, speed and quality. • There is also a Japanese database provider, DDBJ. Christophe Roos - 3/6 Sequence databases & comparison

  4. A look at one entry from EMBL part 1/3 Christophe Roos - 3/6 Sequence databases & comparison

  5. A look at one entry from EMBL part 2/3 Christophe Roos - 3/6 Sequence databases & comparison

  6. A look at one entry from EMBL The feature table of the entry contains several linked items, such as exon-assembly (mRNA) and coding sequence (CDS). There are also cross-references to other databases part 3/3 Christophe Roos - 3/6 Sequence databases & comparison

  7. A look at one entry from SwissProt The eyeless gene: a master regulatory gene in eye formation Christophe Roos - 3/6 Sequence databases & comparison

  8. The effect of the eyeless gene • The eyeless gene is a master regulatory gene in eye formation • When it is absent, no eyes are formed • When it is present where it should not, it induces eye formation Normal Overexpressed in antennae and wings Absent Christophe Roos - 3/6 Sequence databases & comparison

  9. A look at one entry from SwissProt Part 2: the annotations about the function and location Christophe Roos - 3/6 Sequence databases & comparison

  10. A look at one entry from SwissProt Part 3: The feature table and the amino acid sequence Christophe Roos - 3/6 Sequence databases & comparison

  11. A look at one entry from SwissProt The eyeless gene is also called PAX6 and can be found in several species: birds, mammals, reptiles, fish, invertebrates Christophe Roos - 3/6 Sequence databases & comparison

  12. Sequence comparison - Why? • Function by analogy: If sequences are conserved their function is probably also conserved. • Functional domains: If some parts of the sequences are more conserved than other parts, there must be an underlying biological reason for it. • Establishing relationship/differences in function: By quantification of sequence relationships it is possible to estimate function of novel genes • Establishing relationship between species Christophe Roos - 3/6 Sequence databases & comparison

  13. Sequence comparison – how? • Compare two sequences of similar length • Compare two sequences of very different length • Compare several sequences • Allow gaps or not? • Scoring: yes-no or good-intermediate-bad • The best or all above a threshold? Christophe Roos - 3/6 Sequence databases & comparison

  14. Sequence comparison – metrics gap match • The scoring matrix • The score for a match • The penality for a mismatch • The penality for the insertion of a gap (gap-open) • The penality for elongating a gap (gap-length) • Local or global similarities ? GA-CGGATTAG GATCGGAATAG mismatch Christophe Roos - 3/6 Sequence databases & comparison

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