8/22/2023 0 Comments Snapgene vs benchling![]() ![]() But N/ ns may alternatively represent ambiguous nucleotides, indeed this is the IUPAC specification.Īlso note occasionally (although fortunately rarely) X/ x is used to represent ambiguous nucleotides or “hard-masked sequences” too. N and n nucleotides may represent “hard masked sequences”, where interspersed repeats and low complexity sequences are replaced by Ns. ![]() However, there are other uses for lower/upper case letters, for example, Ensembl have used upper/lower case letters to represent exonic and intronic sequences respectively. Note that larger repeats, such as sizable tandem repeats, segmental duplications, and whole gene duplications are not generally masked. Lower case letters are most commonly used to represent “soft-masked sequences”, a convention popularised by RepeatMasker, where interspersed repeats (which covers transposons, retrotransposons and processed pseudogenes) and low complexity sequences are marked with lower case letters. The use of lower/upper case letters and N/ n letters in genomes sequences is not completely standardised and you should always check the specification of the resource you are using. It being replaced by 'n' is likely an artifact of the repeat-masking software where it soft-masks an 'N' by an 'n' to indicate that portion of the genome is likely a repeat too. 'N's represents no sequence information is available for that base. UCSC uses Tandom Repeat Finder and RepeatMasker for soft-masking potential repeats. There is no uncertainty whether a particular base is 'A' or 'G', just that it is part of a repeat and hence should be represented as an 'a'. Soft-masking is done after determining portions in the genome that are likely repetitive. How confident can I be about the sequence in these regions?Īs you can be about in non soft-masked based positions. An important use-case of these soft-masked bases will be in homology searches: An atatatatatat will tend to appear both in human and mouse genomes but is likely non-homologous. These repetitive elements are soft-masked by converting the upper case letters to lower case. Human genome, for example, has (at least) two-third repetitive elements. What does this soft masking actually mean?Ī lot of the sequence in genomes are repetitive. ![]()
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