Alleloscopeallele figures and predicted protein consequences

Each line gene <name> <length> opens a block. Everything that follows (exons, guides, alleles, protein) belongs to that gene until the next gene line. Blocks are stacked from top to bottom.

exon <start> <end>
guide <name> <start> <end>
allele <name> <lesion>... with del start end, ins pos bp, sub start end, snp pos. A word without spaces after a lesion replaces its caption
protein <aa> / domain <name> <start> <end> / trunc <name> <aa> [<first changed residue>]: the changed part is drawn in orange on the protein bar. The Write protein and trunc lines button fills in these numbers, and the protein line, from the translation. An allele whose lesions remove or add a multiple of 3 nt in the exons is in frame: if its trunc line gives the expected length (protein minus the deleted aa), its protein is drawn full length with the deletion in place
scale shared or scale independent (global line): one scale set by the longest gene, or each gene uses the full width

Labels on the figure can be dragged with the mouse. Each move is written at the bottom of the text as nudge <key> <dx> <dy>, so it is kept with the project file and applied to the SVG export.

The exon lines are taken as the CDS: they are spliced and translated as they are, from the first nucleotide of the first exon. No reading frame is searched for or corrected. If something does not add up, it is reported under the boxes, without changing anything.

strand -: the pasted sequence is the reverse complement (the coordinates stay those of the gene).

To predict the mutant protein, give the inserted sequence rather than its length: ins 925 GATTACA, sub 3000 3010 ACGT..., snp 1220 G>A. With a length only (ins 925 7) the frameshift is known but the residues at the insertion point are not: they are shown as X.

A line starting with # is a comment.