User Guide To Display of Gapped Alignments

> ### ACEDB Version 4_9

> # User Guide To Display of Gapped Alignments

> ## Gapped Alignments

> Acedb now supports the storage and display of gap information with alignments.

> The Homol tag in ?Sequence and ?Protein now has a model which looks like this:

>     Homol DNA_homol ?Sequence XREF DNA_homol ?Method Float Int Int Int Int #Homol_info
>           Pep_homol ?Protein XREF DNA_homol ?Method Float Int Int Int Int  #Homol_info
>           Motif_homol ?Motif XREF DNA_homol ?Method Float Int Int Int Int #Homol_info

> and the Homol-info class looks like this:

>     #Homol_info Segs #Match_seg     // old way to give gapped alignment -  used in pephomolcol for Belvu call
>                 Align Int UNIQUE Int UNIQUE Int     // correct way to give gapped alignments for FMAP
>                  // for each ungapped block, self_start target_start [length]
>                  // if no length then until next block (so no double gap)
>                  // if no Align assume ungapped
>                 AlignDNAPep Int UNIQUE Int UNIQUE Int
>                 AlignPepDNA Int UNIQUE Int UNIQUE Int
>                  // These two tags are analogous to Align, but scale length
>     	     // for the case of a dna alignment to peptide or vice-versa.

> This system is backwards compatible since if the Homol_info data is not present, the Homologies are interpreted as before. (For reference, the Float parameter is a score and the four Ints are start and end co-ordinates in this sequence followed by start and end coordinates in the homologous sequence.

> The gap information is stored as blocks of ungapped alignment. This is probably best illustrated by example:

>     Homol DNA_homol somesequence somemethod 100 2732 2809 29233 29310 Align 2732 29233
>                                                                       Align 2742 29253
>                                                                       Align 2752 29273
>                                                                       Align 2762 29276

> Gives and alignment which looks like this:

>                 2732      2741      2742      2751      2752     2762                                    2809
>     self     ----|---------|.........|---------|.........|---------|------------------~~-------------------|-----

>     target       |-------------------|-------------------|--|......|------------------~~-------------------|
>                29233               29253              29273 29275 2976                                  29310

> The third (length) integer is only required when the end of a gap in one sequence coincides with the start of a gap in the other:

>     Homol DNA_homol somesequence somemethod 100 2732 2809 29233 29310 Align 2732 29233 10
>                                                                       Align 2752 29253

>                 2732      2741      2742           2752
>     self     ----|---------|.........|--------------|-------

>     target       |-------------------|..............|----------

>                29233               29252           29253

> ## Displays

> The gaps are not displayed in the fMap, but they are displayed in blixem.

> Gaps in the query sequence (ie where there are bases in the target with corresponding bases in the query) are shown by omitting the un-matched bases and drawing a vertical red bar. Gaps in the target sequence are shown with dots.

> ## Peptide homolgies

> For homologies of DNA versus Peptide, the two sets of coordinates need to be scaled, since a block length of x in amino acid residues corresponds to 3x in DNA bases. To tell acedb when and how to scale, use the AlignDNAPep and AlignPepDNA tags. For instance in a DNA object, to record a homology to a peptide, do:

>     Homol Pep_homol  somepeptide somemethod 200 2777 2699 100 133 AlignDNAPep 2777 100
>                                                                               2753 104
>                                                                               2738 120

> ### ACEDB Version 4_9

> Last modified: Wed May 16 10:29:36 BST 2001