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- Installing the Perl API
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Alignment blocks
In this presentation, you are shown how to access alignment blocks in the Ensembl database.
Exercise 2
A GenomicAlignBlock represents an alignment between two or more regions of genomic DNA. Within these blocks every region of genomic DNA is represented by a GenomicAlign object.
- Print the LASTZ-NET alignments for pig chromosome 15 with cow (using pig coordinates 105734307 and 105739335).
Hint: Use the MethodLinkSpeciesSet adaptor fetch_by_method_link_type_registry_aliases() method (e.g. $mlss_adaptor->fetch_by_method_link_type_registry_aliases("LASTZ_NET", ["pig", "cow"])).
You will need a *core* slice for pig chromosome 15.
Get a GenomicAlignBlock adaptor and use the fetch_all_by_MethodLinkSpeciesSet_Slice() method to retrieve the genomic_align_block object(s).
Use the GenomicAlignBlock restrict_between_reference_positions() method to “restrict” the genomic_align_block between base pairs 105734307 and 105739335.
Finally, print the alignment using the GenomicAlignBlock get_SimpleAlign() method (use AlignIO to format the output alignment). - Change the above example so that it prints the 13-way eutherian mammal (EPO) multiple alignments.
Hint: Use the MethodLinkSpeciesSet adaptor fetch_by_method_link_type_species_set_name() method (the method_link_type is “EPO” and the species_set_name is “mammals”).
