Active ORF - the ORF which sequence is currently displayed in ORF display frame, highlighted on Sequence Viewer graphics and ORF table. ORF can be made 'active' by clicking on it on graphics, or ORF table row.

Active ORF protein sequence can be sent to NCBI SmartBLAST and BLAST (SmartBLAST and BLAST buttons under ORF#)

Active ORF can be marked/unmarked by Mark / Unmark button, 'Space' or 'Ins' keys.
Double click on any ORF table row marks/unmarks this row ORF and makes it active.

The marked ORFs are highlighted in the table and framed on graphics.

Marking an ORF puts it into a marked set, which can be

• downloaded (Download marked set button) in selected format (Protein FASTA / CDS FASTA / ASN.1 / Feature table)
• sent to the NCBI protein BLAST (BLAST under Marked set) to compare against pre-selected BLAST database (UniProtKB/Swiss-Prot (swissprot) / Reference proteins (refseq_protein) / Non-redundant protein sequences (nr)). This pre-selection can be changed on BLAST parameter setting page.
• used to retrieve the title of SmartBLAST best hit (SmartBLAST best hit titles... under Marked set)

Selection Mark subset... allows to select ORF sub-set to mark (All ORFs / Longest ones (up to 10) / Strand(+) / Strand(-)) or Unmark all.

Display ORF as... Select ORF sequence display: Protein sequence (default) / Nucleotide sequence / CDS translation (both nucleotide sequence and corresponded amino acids). Input data for BLAST doesn't depend on sequence display choice, it is always ORF protein sequence.

Six-frame translation... Related independent functionality options:

• Display six-frame translation opens a draggable widget, displaying processed by ORFfinder sequence fragment and its six-frame translation with marked ORFs. Does not block any other ORFfinder functionality. Download option is provided (not in IE).
• Add (Remove) six-frame translation track updates Sequence Viewer (graphics) display accordingly

For Sequence Viewer (graphics) functionality details see its own Help link in graphics upper right corner.