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Using sequence case to encode intron/exon information

I've heard that sometimes sequences are stored in files partially lowercase and partially uppercase, with the intent that lower- or upper-case regions indicate introns or exons.

Is this a common practice? Are there file formats that explicitly support this type of encoding? Google hasn't yielded anything, but I might just be searching for the wrong things.

sequence
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written by anderspitman • anderspitman

1 answer

Yes it is common practice, but it is not a standard.

Another common usage for lower case is to indicate softmasks, that is, lower case sequences should not be processed/analyzed.

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written by h.mon h.mon

Can you link to any examples where the convention is explained?

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written by anderspitman • anderspitman

Lower-case as exon-intron: this paper, which refers to this (or this) database; or see this server to generate pretty graphics of gene structure.

Lower case for soft-masking: see USEARCH manual or Blast lcase_masking parameter.

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written by h.mon h.mon

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