'SHOW_CDS_FEATURES=on' option allows the BLAST server to display the translation of CDS (annotated open reading frames) features found in the database entries in the Pairwise alignment. Using the CDS feature from the database entry and the alignment as a guide, the BLAST server will also display the translation of potential CDS features in the query.
The 'SHOW_LINKOUT=on' indicates the availability of additional information for database entries through colored icons. The icons are hyperlinked to entries in other databases and will provide additional information on the function, sequence cluster, 3D structure, and expression for the matching entries.
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| Figure 6.11 Alignment with linkout icons and CDS translation. |
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In the example result above with 'NEW_VIEW=flase', the translations of a CDS on the query (marked by a blue box) and database entry (marked by a pink box) are displayed. The Linkout icons indicate that additional information is available for this database entry. In addition, we used 'MASK_CHAR=2', and 'MASK_COLOR=2', so we also display the masked region in red lower case letters.