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Edit sequence

'Edit sequence' displays the sequence of the selected contig in detail. It consists of three parts: 'Contig sequence', 'Open reading frames' and 'Selected sequence'

It also contains its own right-click menu.

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Contig sequence
This part displays the contig sequence. Left-clicking on a base will mark it in red, also a red line appears at the associated position in the 'Open reading frames'-canvas. Right-clicking on a base will open a menu for modifying it.
The blue bars above the bases represent their coverage to a maximum of 30. Then there are green, orange or red squares directly above the bases, these show conformity of the 'read'-bases, which lie at this position. If more than 90% of the 'read'-bases are equal to the 'contig'-base the square is green, it is orange by 60% to 90% and below 60% it is red.
Directly below the bases the amino acids of a selected ORF can be displayed. At last there are six lines, which represent the six frames of the nucleotide sequence. On the lines can appear blue or red regions, these are markers for start (blue) and stop (red) condons in the accordant frame.

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Open reading frames
The yellow bar in the canvas represents the contig sequence. There is a right-click menu associated with this bar. Then there are six levels, which represent the different frames of the contig. On each level the ORFs are shown in green, start codons in blue and stop codons in red.
Clicking somewhere in the canvas will move the red line to that position, it will also mark the associated base in the 'Contig sequence'. Clicking on a ORF will mark it in a dark green, the sequence of the ORF will appear below the 'Contig sequence' and in the 'Selected sequence'-panel.

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Selected sequence
Displays the selected nucleotide or protein sequence.


Right-click menu

The two right-click menus of 'Edit sequence' contain mainly special function, but also some of the standard right-click menu.

Add to blast
Coverage
Delete
Insert
New sequence
Refresh
Replace with
Search
Show complementary strand
Translate whole frame

Add to blast
See 'Add to blast' in right-click menu.

Coverage
See 'Coverage' in right-click menu.

Delete
Deletes the selected base from the contig sequence. This is no permanent chance to the contig.

Insert
Insert a new base at the selected position of the contig sequence. This is no permanent chance to the contig.

New sequence
See 'New sequence' in right-click menu.

Refresh
Redraws the 'Open reading frames'-canvas, e. g. to fit a new window size.

Replace with
Replaces the selected base in the contig sequence. This is no permanent chance to the contig.

Search
Opens a search dialog, which allows to search for patterns in a reference string. The search results will highlighted.
This option is available for the 'Contig sequence'-part and the 'Selected sequence'-panel.
Show complementary strand
Displays the complementary strand of the contig sequence in the 'Selected sequence'-panel.

Translate whole frame
Translates the whole frame from nucleotides into amino acids. Stop condons will appear as '*'.


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