[EMBOSS] Candidia

Nermin Celik n.celik00 at gmail.com
Tue Apr 27 03:13:08 UTC 2010


Hi,

I would like to translate yeast Candida albicans nucleotide sequence into
protein sequence using transeq. However I got confused with the '-table'
values.

The taxonomy information for candidia is:
*Lineage*<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=160764&lvl=3&lin=s&keep=1&srchmode=1&unlock>
(full): root<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Root&id=1&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
cellular organisms<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=131567&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Eukaryota<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=2759&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Fungi/Metazoa group<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=33154&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Metazoa<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=33208&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Eumetazoa<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=6072&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Bilateria<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=33213&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Coelomata<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=33316&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Deuterostomia<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=33511&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Chordata<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=7711&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Craniata<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=89593&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Vertebrata<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=7742&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Gnathostomata<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=7776&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Teleostomi<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=117570&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Euteleostomi<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=117571&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Actinopterygii<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=7898&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Actinopteri<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=186623&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Neopterygii<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=41665&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Teleostei<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=32443&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Elopocephala<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=186624&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Clupeocephala<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=186625&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Otocephala<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=186634&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Ostariophysi<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=32519&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Otophysi<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=186626&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Cypriniphysi<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=186627&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Cypriniformes<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=7952&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Cyprinoidea<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=30727&lvl=3&lin=f&keep=1&srchmode=1&unlock>;
Cyprinidae<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=7953&lvl=3&lin=f&keep=1&srchmode=1&unlock>

(retrieved from NCBI).

Based on the above information which '-table' value is best/suitable?

Nermin



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