Fig. 4

Workflow for creating a database of mobile elements from algae. Clockwise from top left: Keyword search is done in blncbi query builder. In the nucleotide search field, the user chooses Organism and types in “algae”. Since automated extraction of features is desired, the boolean operator AND is chosen, and the second search field set to “Feature Key mobile_element”. Thus, only GenBank entries with the mobile_element features key would be found. For more complex queries, left and right parentheses could be chosen to group terms together. Since genomic sequences are desired, the Molecule field is set to genomic. When the search is launched, the Entrez search expression “algae [ORGN] AND mobile_element [FKEY] AND biomol genomic [PROP] AND 1:500000[SLEN]” is sent to NCBI using ncbiquery.py, a Python script implementing the NCBI Eutils API. The Entrez document summary for 1383 GenBank entries matching the expression is retrieved to a new blncbi object. To better understand the species distribution of mobile elements, the user sorts by species. GenBank entries are retrieved to a bldna object. From the GenBank entries, FEATURES extracts 37,484 mobile_element sequences to a new bldna object