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Tutorial by Ebbe S. Andersen

== Formats and starting SARSE ==

SARSE loads fasta, widetext and col files. The col file format is used by the editor to attach various informations to each position of your alignment. The rnadbtools package contains some format converters that you can use to change the format of your data into the col format e.g. from ClustalW:

 prompt> aln2col alignment.aln > alignment.col 

Your file is now ready to be loaded in the SARSE program typing SARSE on the command-line:

 prompt> SARSE 

You will now see the editor window and you can use the File/New menu to create a new project. Alternatively, you can start SARSE giving projectname and file name on the command-line:

 prompt> SARSE --project=HIV1-leader --file=alignment.col 

You should see the SARSE editor window looking something like this:

[[Image:tutorial8.gif]]

== SARSE: Annotation and editing ==

The pairingmask can either be based on literature, experiment or prediction. In the first two cases you have to enter the known pairingmask, in the latter case you can make the Pfold program determine a common pairingmask for your alignment (go to the Pfold section). The RNA sequence that you have information about from the literature or from experiments will be referred to here as the reference sequence. Select the positions in the reference sequence that are known to be paired, then click Pair columns . You will be asked which symbol to use in the pairingmask. Write a symbol (will only accept symbols A-Z, a-z and 0-9), click ok, and the program will now write your symbol in the pairingmask and set all bases in the selected columns that can pair to upper case. SARSE uses upper case and lower case to indicate paired and single stranded bases, respectively. You can also change symbols directly in the pairingmask by Change symbol and then use Fit alignment to pairingmask to change the annotation of the sequences below.

SARSE contains several features that make it easier to edit a large RNA structural alignment. You use the left mouse button for the basic selection of bases. There are two ways of moving bases within an alignment: 

(1) You make a selection with the left mouse button and use the right mouse button to drag the selected bases to a new position. The selected block can only be moved in gap regions:

[[Image:tutorial7.gif]]

(2) The Move left/Move right option in the Edit menu allows you to move bases long distance. You make a selection of the bases that you want to move and the gaps that you want to move them across. Then using the Move left/Move right the bases will be moved from one end of the selection to the other:

[[Image:tutorial6.gif]]

Another selection option is Single select or Double select. The Double select option automatically selects paired bases. Often stems are far apart in sequence and SARSE offers the Split view that allows you to see the two stem parts at the same time. In Split view the Double select function will automatically align the two windows to the specific base pair chosen.