Genome Analysis Software Site

in silico biology, inc.

IMC W713 Genome Analysis Tab Pane Description

In the Genome Analysis tab pane, set the base length stage of the ORF candidate, the maximum display dot number of the dot plot, the maximum base length recognized as intron in gene mapping (mRNA sequence and amino acid sequence mapping) You can set the genetic code table to use, specify prokaryotic or eukaryotic.

ORF Extraction Setting section:

The ORF candidate has a high probability that a gene whose base length is long is a true gene. For this reason, in the IMC, the base length step of the ORF is divided into three, so that annotation can be performed separately. The threshold at this stage can be set by the user.

Long ORF> = text field: This text field specifies the minimum base length of the ORF candidate feature identified as ORF_Long.

Middle ORF> = text field: This text field specifies the minimum length of the ORF candidate feature identified as ORF_Middle.

Short ORF> = text field: This text field specifies the minimum length of the ORF candidate feature identified as ORF_Short.

Transl_table pull-down menu: Select the genetic code table used for amino acid translation.

DotPlot section:

Maximum Number of Dots on the Plot text field: Enter a positive integer. Specify the maximum value of the dot to be printed on the dot plot. Even if there is a number of dots that exceeds the maximum value, dots that exceed the maximum value will not be hit. Note that this setting can be changed in the Dot Plot Drawing Dialog.

Mapping section:

When mapping mRNA, cDNA, or amino acid sequence, specify the maximum base length to be regarded as an intron when the sequence is interrupted by intron.

Maximum Length of Intron text field: Enter a positive integer. If the length of the intron exceeds this specification, it will not be mapped.

Translation section:

Transl_table pull-down menu: Select the genetic code table to be used for amino acid translation from the pull-down menu.

Type Prokaryote Eukaryote Toggle Radio Button: Turn on either prokaryotic or eukaryotic. This will change the method of amino acid translation processing.

For Feature Setting common operation buttons, please click here.

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