I would like to improve the Jalview editor. This mean, I would like to be able to read a fasta-file of an alignment including the secondary structure, the fasta-file looks like this:
This means, we have a number n of differents proteins sequence which are all aligned and in between we have the secondary structure for each sequence. I hope, you understand what I mean.
Thanks very much for this suggestion. The format that you describe would
be quite easy to implement in Jalview - I am also aware that the CBS at
the Danish Technical University developed a very similar model for
annotating sequences with the results of their predictors, and it would
be useful for jalview to read this kind of file.
Are you a java programmer ? I can give you some pointers on how to
implement this, if you are interested in this.
Alternately, you could try generating a Stockholm format file. This
format allows secondary structure to be specified, and is one of the few
formats currently understood by Jalview which also allow features and
secondary structure annotation to be specified in the same file.
Jim
Massassi Pepito wrote:
···
I would like to improve the Jalview editor. This mean, I would like to
be able to read a fasta-file of an alignment including the secondary
structure, the fasta-file looks like this:
Prot_1_sequence:
ABDCGJLLKK
Prot_1_secondary_structure
HHHHBBBTTT
Prot_2_sequence:
ABDCGJLLKK
Prot_2_secondary_structure
HHHHBBBTTT
.......
Prot_n_sequence:
ABDCGJLLKK
Prot_n_secondary_structure
HHHHBBBTTT
This means, we have a number n of differents proteins sequence which are
all aligned and in between we have the secondary structure for each
sequence. I hope, you understand what I mean.
Any helps are welcome,
Thanks
Massassi.
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