Look at this nice java-program
or more generically if you like to program perhaps:
Otherwise there are several big commercial packages that among a lot of
other features have the ones you are looking for. i.e VectorNTI from
Peter Frank wrote:
> I am looking for a program for pretty formatting of sequences (not
>> I have several raw sequence data files and they are nothing but
> letters, of course. That way they look pretty dull and it is very hard
> to find any orientation from such a sequence when printed on paper.
> Therefore, the program I am looking for should:
> * be able to perform automatic sequence blocking with selectable
> numbers of characters and columns
> * be able to put position numbers to the left and/or to the right of
> each sequence line
> * perhaps allow formatting of personally selected regions within the
> sequence (however, this is not really necessary since I can also do
> that in any word processor as long as the formatted sequence can be
> exported in text format)
>> I tried this with GeneDoc (which is actually used for alignments,
> thought I'd give it a try anyway) but couldn't get any satisfactory
> results. Maybe I just did not use it right. Is all of the above
> possible with GeneDoc?
> If not, can anyone recommend me a program for the above purpose?