There should be little requirement to split sequences into smaller sub-sequences in EMBOSS, but there may be circumstances where memory usage becomes restrictive when dealing with truly large sequences. In this case, memory usage may be reduced by repeating the analysis several times on split sub-sequences.
If you need to split a large sequence into smaller subsequences so that a non-EMBOSS program can analyse the smaller sequence, it may also be useful to write the sub-sequences into separate files instead of the default EMBOSS behaviour of concatenating them together into one file.
To write the output sequences to separate files, use the command-line switch '-ossingle'.
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The names of the sequences are the same as the original sequence, with '_start-end' appended, where 'start', and 'end' are the start and end positions of the sub-sequence. eg: The name HSHBB would be changed in the sub-sequences to: HSHBB_1-50000 and HSHBB_50001-73308 if they were split at the size of 50000 with no overlap.