AnnHyb's help - Howto



1) How to create a new oligo
2) How to open an oligo
3) How to export an oligo
4) How to export oligo data
5) How to align an oligo with a sequence
6) How to create a new sequence
7) How to search a sub-sequence into a sequence






1) How to create a new oligo

To create a new oligonucleotide,
1) Click the Oligo / New Oligo menu
2) Type the name of the new oligo in the Name edit box
3) Type the oligonucleotide's sequence in the Seq edit box

AnnHyb will determinate the length, the molecular weight, the molar extinction coefficient, the GC percent and the melting temperature of the new oligonucleotide



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2) How to open an oligo

To open an oligonucleotide,
1) Click Oligo / Open Oligo menu
2) Choose the file where you have saved your oligo (the default extention for saved oligo is OLI



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3) How to export an oligo

To save only the selected oligo, click Oligo / Save oligo or Oligo / Save oligo as...
Oligo can be exported in 2 formats: FASTA format and OLI format (AnnHyb). The OLI format contains the salt and primer concentrations for the melting temperature determination while the FASTA format contains only the oligo name and sequence

To save all oligonucleotides in one file, click Oligo / Save all oligo
Multi oligo can be exported in 2 formats: FASTA format and OLA format (AnnHyb). The OLA format contains the salt and primer concentrations for the melting temperature determination while the FASTA format contains only the oligo name and sequence



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4) How to export oligo data

To export oligonucleotide's data in a plain text file, click Oligo / Export oligo data or Export data for all oligo

Example of exporting oligo data


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5) How to align an oligo with a sequence

To align an oligo with a sequence, you must:
create a new oligo.

Select a color for the oligo to search/align.


Click Oligo / Align Oligo with sequences or Oligo / Quicksearch oligo in sequences menu. The "Align" function allow gap opening in oligo or sequence while the "Quicksearch" function not
Check sequences to align in Select sequences window
Click OK to start the alignment
Results are displayed in a window in the Oligo tab

aligned oligo

If you activate the "Automatic check best oligo" option (see Options / Parameters - Align / Quicksearch oligo tab), the aligned oligo are automatically checked if the aligned score is greater than the cut-off

The checked oligo are displayed in a window in the sequence tab with informations on alignment
Oligo are also highlighted on the selected sequence




6) How to create a new sequence

To create a new sequence, click Sequence / New sequence menu
Input the sequence in the Edit window



When have typed all nucleotides, click the Sequence / Done menu
Type a sequence name (mandatory) and additional information about the sequence



The new sequence is added to the left tree view


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6) How to search a sub-sequence into a sequence

Select the sequence to search into, select the Sequence/Quick search for sub-sequence menu option
Type the sub-sequence you want to search
Press the Search button


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