Special rendering for discrepancies between genomic sequence and known RefSeq transcripts/corresponding proteins

In a process of genome annotation known RefSeq transcripts/corresponding proteins are aligned to genomic DNA. Special rendering has been implemented for discrepancies in such alignments.

  • mismatched codons are shown in red color
  • mismatched nucleotide bases are printed over RNA bar
  • mismatched amino-acids are printed over CDS bar
  • deletions are shown as dashes '-' inside of RNA bar and CDS bar
  • insertions are shown as hourglass-like triangles inside of RNA bar and CDS bar

Special case: ribosomal slippage If translation is known to be effected by ribosomal slippage, frameshifts can be seen as shifted (but not colored) codons and corresponding amino acids.

Please download test files for each example. Open each test file with Genome Workbench and open the Graphical Sequence View (right click - Open New View - Graphical Sequence View).

RefSeq coding region with mismatches, deletion, and insertion in the genomic feature compared to the genomic sequence

Test file: Discrepancies in CDS

coding region discrepancy

RefSeq RNA with insertion, deletion, or mismatch in the genomic feature compared to the genomic sequence

Test file: Discrepancies in RNA

rna discrepancy

Ribosomal Slippage with -1 frameshift

Test file: Ribosomal Slippage with -1 frameshift

Ribosomal slippage is represented by an extra "joinvisual" shift of the translated sequence.

Note how NP_001120696.2's AAA(K) codon is shifted relative to NP_001103414.2's AAC(N) because of -1 frameshift.

ribosomal slippage -1 frameshift

Ribosomal slippage with +1 frameshift

Test file: Ribosomal Slippage with +1 frameshift

ribosomal slippage +1 frameshift

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Last updated: 2019-09-16T20:05:09Z