[Biojava-l] Stranded non-contiguous feature looses its strand in a SubSequence

[Stein Aerts]

Does anyone know why, if you make a subsequence, some of the features that
are stranded in the original sequence are not stranded anymore in the
subsequence?
Would there be a workaround?

Example: (embl file and the code I used is in attachment)

features on the original sequence:

ENSG00000114251: prediction|-|31979, 33725 {([31979,32271]),
([33699,33725])}|
ENSG00000114251: exon|-|[36988,37230]|
ENSG00000114251: CDS|-|37181, 38568 {([37181,37238]), ([38459,38568])}|
ENSG00000114251: exon|-|[38459,39310]|
ENSG00000114251: exon|-|[11752,11941]|
ENSG00000114251: prediction|+|[68957,69037]|
ENSG00000114251: prediction|-|[7506,7964]|
ENSG00000114251: prediction|-|[11751,12043]|
ENSG00000114251: exon|-|[77834,77918]|
ENSG00000114251: exon|-|[7510,7965]|
ENSG00000114251: source|+|[1,82918]|
ENSG00000114251: exon|-|[32080,32272]|
ENSG00000114251: prediction|-|[13468,13565]|
ENSG00000114251: prediction|-|36987, 59254 {([36987,37237]),
([38458,38591]), ([42674,42788]), ([43206,43321]), ([45592,45884]),
([46589,46685]), ([59243,59254])}|
ENSG00000114251: prediction|+|73976, 74614 {([73976,74134]),
([74468,74614])}|
ENSG00000114251: exon|-|[36988,37238]|
ENSG00000114251: exon|-|[5001,7965]|
ENSG00000114251: CDS|-|7510, 77918 {([7510,7965]), ([11752,11941]),
([32080,32272]), ([36988,37230]), ([77834,77918])}|
ENSG00000114251: exon|-|[11752,12044]|
ENSG00000114251: prediction|+|16957, 20027 {([16957,17042]),
([19913,20027])}|


features after making a SubSequence of (77718,79918)

ENSG00000114251: exon|-|[117,201]|
ENSG00000114251: source|[1,2201]|
ENSG00000114251: CDS|[117,201]|

Now the last CDS is not stranded anymore. Could the reason be that this CDS
has a joined location in the original sequence? Because the exon still has
its strand.

Thanks & bye,
Stein Aerts.



Ir Stein Aerts
Bioinformatics Research
KULeuven, ESAT-SCD
Kasteelpark Arenberg 10
3001 Heverlee, Belgium
Tel +32-16-32.17.91
Fax +32-16-32.19.70
http://www.esat.kuleuven.ac.be/~dna/BioI/