EASER

EASER retrieves and prepares Ensembl-defined genomic features and sequences (coding sequences (CDS) and genomic sequences) using specified identifiers and relationship types to assemble customizable datasets for genomic analyses.

Key Features:

• Ensembl retrieval: Downloads and prepares Ensembl-defined genomic features associated with user-supplied identifiers.
• Sequence types: Retrieves coding sequences (CDS) and genomic sequences.
• Relationship-type selection: Supports specified relationship types among genomic elements to control which features are retrieved.
• Organism selection: Allows retrieval across all available organisms or a user-specified subset of organisms.
• Script-based automation: Automates downloading and dataset preparation via scriptable workflows.
• PyCogent integration: Operates within the PyCogent library to enable compatibility with PyCogent-based analyses.

Scientific Applications:

• Comparative Genomics: Facilitates retrieval of homologous sequences across organisms for evolutionary and conservation analyses.
• Functional Genomics: Provides genomic features and sequences needed for gene function, expression, and mutational studies.
• Metagenomics: Assembles sequence datasets spanning multiple organisms to support analyses of complex microbial communities.

Methodology:

Script-based interaction with Ensembl databases to download and prepare sequence data; retrieval of genomic features tied to user-defined identifiers; support for multiple relationship types; integration within the PyCogent library.