#Please insert up references in the next lines (line starts with keyword UP)
UP	arb.hlp
UP	glossary.hlp
UP	species.hlp

#Please insert subtopic references  (line starts with keyword SUB)
#SUB	helix.hlp
SUB	ecoliref.hlp

# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}

#************* Title of helpfile !! and start of real helpfile ********
TITLE		SAI (Sequence associated information)

DESCRIPTION	The main database divides all sequences into two groups:

                    1. sequences of species -> stored in alignments of species
                    2. all other sequences (masks, filters, profiles) -> stored in alignments of SAIs

		You should keep the number of SAIs limited for you cannot search SAIs.

SECTION         Edit SAIs

                * LINK{ad_extended.hlp}
                * LINK{e4_modsai.hlp}
                * LINK{saicalc.hlp}

SECTION         Visualize SAIs

                * LINK{visualizeSAI.hlp}
                * LINK{saiProbe.hlp}

SECTION         IMPLEMENTED SAIs

		ECOLI

                        A copy of the E.coli sequence (see LINK{ecoliref.hlp}).

                        It is used to convert the absolute alignment position into
                        an E.coli-based position and vice versa.

                        Note:
                            * you may use any other sequence instead of ECOLI.
                            * the name displayed in ARB_EDIT4 can be modified under Properties/NDS
                            * see LINK{sp_sp_2_ext.hlp} for how to generate.

		HELIX_NR

                        Helix Numbering

		HELIX

                        and Helix template (see LINK{helix.hlp})

                CONSENSUS

                        custom consensus sequence (see LINK{consensus.hlp})

SECTION         Additional information about SAI

                * LINK{accessibility_sai.hlp}