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Variants view

To see the Variants view, you must first perform a multiple alignment. When the alignment is complete, the Variants view opens showing a Compute Variants button. Click the button to calculate the variants.

If you have specified a reference sequence, variants are calculated against the reference. If no reference sequence was specified prior to alignment, variants are calculated against the consensus sequence. Pressing the button results in a table of variants being displayed in the view.

Once the Variants view has been enabled, you can access it by clicking the Variants tab or by choosing View > Variants > Show.

Each row in the Variants table represents a variant in an aligned sequence.

The table columns are described below. Some columns may only be available for amino acid sequences and others for nucleotide sequences.

Column Name Description
Peptide Impact
Ref Aliphatic The reference’s relative volume occupied by aliphatic side chains (alanine, valine, isoleucine and leucine) as calculated using the method of (Gasteiger et al. 2005). The aliphatic index predicts regional stability by calculating the relative volume occupied by aliphatic side chains and is a positive indicator of globular protein thermostability. Detailed information about this method is available on the ExPASY website.
Ref Charge The reference’s pH-dependent sum of charges in molecules, assuming a pH of 7. DNASTAR developed this method using the pK tables of Lehninger, 2005.
Ref Hydropathy The reference’s hydropathy value as calculated using the approach of Kyte and Doolittle, 1982. Residue hydropathy assignments are derived from water-vapor transfer free energies and the interior-exterior distribution of residue side-chains.
Ref Instability An estimate of the stability of the reference protein in a test tube, calculated using the approach of Guruprasad et al., 1990. This approach predicts regional instability by calculating the weighted sum of dipeptides that occur more frequently in unstable proteins when compared to stable proteins. Detailed information about this method is available on the ExPASY website. An instability index less than 40 predicts a stable protein, whereas values higher than 40 denote a potentially unstable protein.
Ref pI The reference’s isoelectric point, the pH at which the residue carries no net electrical charge. This is calculated by using the pKa tables from Lehninger et al., 2005 to identify uncharged regions at a given pH, which have an increased potential to aggregate if surface exposed.
Var Aliphatic The variant’s relative volume occupied by aliphatic side chains (alanine, valine, isoleucine and leucine) as calculated using the method of (Gasteiger et al. 2005). The aliphatic index predicts regional stability by calculating the relative volume occupied by aliphatic side chains and is a positive indicator of globular protein thermostability. Detailed information about this method is available on the ExPASY website.
Var Charge The variant’s pH-dependent sum of charges in molecules, assuming a pH of 7. DNASTAR developed this method using the pK tables of Lehninger, 2005.
Var Hydropathy The variant’s hydropathy value as calculated using the approach of Kyte and Doolittle, 1982. Residue hydropathy assignments are derived from water-vapor transfer free energies and the interior-exterior distribution of residue side-chains.
Var Instability An estimate of the stability of the variant protein in a test tube, calculated using the approach of Guruprasad et al., 1990. This approach predicts regional instability by calculating the weighted sum of dipeptides that occur more frequently in unstable proteins when compared to stable proteins. Detailed information about this method is available on the ExPASY website. An instability index less than 40 predicts a stable protein, whereas values higher than 40 denote a potentially unstable protein.
Var pI The variant’s isoelectric point, the pH at which the residue carries no net electrical charge. This is calculated by using the pKa tables from Lehninger et al., 2005 to identify uncharged regions at a given pH, which have an increased potential to aggregate if surface exposed.
ΔAliphatic Var Aliphatic minus Ref Aliphatic.
ΔCharge Var Charge minus Ref Charge.
ΔHydropathy Var Hydropathy minus Ref Hydropathy.
ΔInstability Var Instability minus Ref Instability.
ΔpI Var pI minus Ref pI.
Variant
Codons When a CDS feature is present on the reference sequence at the position of a variant, this column displays information about the codon change. All information in this column is a compilation of data from other available data columns, regardless of whether or not those columns are currently displayed. The information appears as: Ref Protein Pos followed by Ref Translation:Ref Codons → Var Translation:Var Codons. Example: 5 S:TCA → L:TtA.
Cons Pos The nucleotide position where the variant occurs in the gapped consensus, as measured from the left end of the alignment block.
Feature Distance The distance from the nearest known feature, if any. A positive number denotes that the position is upstream of the nearest known feature, while a negative number means that it is downstream of the feature. A zero value means that the position is inside the span of a coding feature (including introns).
Feature Name Name of the containing or nearby coding feature, if any.
Impact The impact of the variant or indel on the genome, displayed as one of the following values:

  • Synonymous – No amino acid changes.

  • Non Synonymous – Amino acid substitution only.

  • Nonsense – Amino acid to translational stop.

  • Frameshift – An indel within a coding region and which is not a multiple of 3, thereby changing the reading frame.

  • No Start – A change that disrupts the start codon.

  • No Stop – A change that converts a stop codon to an amino acid, and thereby extends the reading frame.

  • Inframe Insertion – An insertion within a coding region whose length is divisible by 3.

  • Inframe Deletion – A deletion within a coding region whose length is divisible by 3.

    If sorting by the Impact column, the column is ordered alphabetically, except that Noncoding appears at the bottom of the list.
Length The total length of the variant, whether it consists of a 1-base SNP or a multi-base insertion or deletion.
Ref Bases The base(s) found at that position in the reference sequence.
Ref Coding Pos The DNA position in the coding sequence for the reference protein.
Ref Codons The corresponding reference-sequence codons, for variants aligned with a coding feature in the reference sequence.
Ref Pos The nucleotide position where the variant starts, as measured from the 5’ end of the reference sequence.
Ref Protein Pos The amino acid position in the reference protein where the variant has been detected. The reference protein is derived from a translation of the cDNA features in the reference sequence.
Ref Translation The translation of the Ref Codons. Uses the genetic code, if any, identified by the coding feature. Otherwise, uses the standard genetic code.
Sequence The name of the sequence that contains the variant, when compared to the designated reference sequence.
Strand The strand of the coding feature on the reference sequence. A right-facing arrow (>) denotes the forward strand, while a left-facing arrow (<) denotes a reverse-oriented strand.
Type Specifies the variation type. SNP is only used for nucleotide sequences and Sub (stitution) is only used for protein sequences. Del (etion) or Ins (ertion) can be used for either sequence type and is followed by the length of the deletion/insertion.
Var Bases The base(s) found at that position in a non-reference sequence.
Var Codons The codons in the variant sequence containing the variant residues, for variants aligned with a coding feature in the reference sequence.
Var Pos The nucleotide position where the variant starts, as measured from the 5’ end of the sequence containing the variant.
Var Translation The translation of the Var Codons. Uses the genetic code, if any, identified by the coding feature. Otherwise, uses the standard genetic code.


Tasks pertaining to the Variants view:

Task How to…
Select or deselect all variant rows in the table Select all variants using Variants > Select > Select All. Remove the selection using Variants > Select > Select None. Selection is often followed by using a copy command.
Select individual variant rows Use the mouse or use Shift+click or Cmd/Ctrl+click. Selection is often following by using a copy command.
Select all rows except for the currently-selected rows After first selecting one or more rows (see above), choose Variants > Select > Invert Selection. Selection is often following by using a copy command.
Sort variants Click on a column header to sort variants by the values in that column. Some columns are sorted alphabetically, some numerically, and some with custom orders. To sort by multiple columns, press the Alt key (Windows) or the Option key (Mac) while clicking additional column headers.

Note that in Lasergene 17.4 (the first version featuring this view), sorting by sequence name may be slow.
Navigate to a variant Click the variant in the variants table. The Sequences view and Overview will navigate to that variant.
Navigate to a variant and show the Sequences view Double-click the variant in the variants table. The Sequences view will appear. The Sequences view and Overview will navigate to that variant.
Choose columns that should appear in the view and their order Press the Choose or rearrange columns () tool in the top right of the view. Items in the list on the right are the columns currently being displayed and the order in which they appear. Make selections and use the up/down and right/left arrows to add, subtract, and reorganize these columns as desired.
Change the font display Click the Show Style tool () to add a row below the current header that lets you change the look of the font in this table.



You can use the drop-down menu to select a different font, change the font size, or specify the use of bold (“B”) or italic (“I”) fonts. To minimize the row, click the tool again or use the Collapse tool (inverted ‘v’) on the right of the row.
Export data from the view Click the Export Data tool (), a shortcut to the File > Export Data subcommands. See Export data to a file.

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