Sequence case converter
Uppercase, lowercase or toggle case for DNA, RNA and protein. FASTA headers are kept as they are.
Uppercase, lowercase or toggle case for DNA, RNA and protein. FASTA headers are kept as they are.
The letters mean the same in either case, so case is free to carry a second layer of information. Genome browsers and assemblers use soft-masking: repeats and low-complexity regions found by RepeatMasker are written in lowercase while the rest stays in capitals, so an aligner can ignore them without losing the sequence. Cloning plans use the same trick for primer tails, restriction-site overhangs, tags and linkers, and exon and intron boundaries are often shown by switching case at the junction. Converting or toggling the case lets you strip that annotation for a tool that trips over mixed case, or invert it to bring the marked region into focus.
Header lines starting with > and comment lines starting with ; are copied through unchanged, so record names, accessions and descriptions keep their case. Everything else is treated as sequence and converted line by line, with line breaks, spaces, numbers and gap characters left exactly where they are. A multi-record file comes out with the same records in the same order.
To remove spaces, numbers, line breaks and alignment gaps as well, use thegap cleaner. To re-wrap a sequence into numbered blocks for a figure or a manuscript, use the sequence formatter.
No. A, C, G and T mean the same in either case, and every alignment or translation tool reads them identically. Case is only an annotation layer: lowercase is used by convention for soft-masked repeats, introns, primer tails or anything the author wants to set apart.
No. Lines starting with > (and ; comment lines) are passed through exactly as they are, so record names and descriptions keep their original case. Only sequence lines are converted.
It swaps the case of every letter: uppercase becomes lowercase and lowercase becomes uppercase. It is the quickest way to invert a soft-masked sequence so the masked part is the one in capitals.
Yes. The converter changes letters only and does not check the alphabet, so DNA, RNA and protein sequences are all handled the same way.
A sequence in which repeats and low-complexity regions are written in lowercase instead of being replaced by N, which is hard masking. Genomes from Ensembl, UCSC and RepeatMasker are distributed this way, and aligners such as BLAST can skip the lowercase part when seeding. Converting to uppercase removes the masking; the bases themselves do not change.