Hello, I'm having difficulty using artemis with certain files from
NCBI. I looked at the documentation and the mailing list archives and
couldn't find anything that looked like it might address my issue.
Here is an example file that illustrates my problem:
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi??
db=nucleotide&val=AY178864
a chloroplast genome from Adiantum capillus-veneris.
The file seems to load correctly in Artemis v8. However, if I try to
export or view the peptide sequence of some certain CDS their
sequences doesn't seem correct. For instance, in the example file I
selected the ndhB CDS in artemis, then "View Amino Acids Of Selection
as FASTA". This is the incorrect sequence that it displays:
>ndhB spans the LSC and IR with the intron across t - 389: 150129
MW: 54568.566
SPTPVVAFFSVTSKVAAPASFTRLFGLIFPYFSNEWHVAVGLLATFSMILGNLIAVTQRS
VKRMLAYPSISQIGYIMIGVLSADSGNGYASMITYTFIYILMNLGTFARITPFGLRTGTD
NIRDYAGLYMKDPVLTFSSVLRSPSLGGMPPPSGFFGKLYLFWHGWKAGLYSSVPVALVT
SVISIYYYLKIIKSMFTGKSGRSDTPLNSRQNSLVSLSISISKNSLEIAMIIRALASTLS
GIFIDPIIEITRNTFF+TNDINLFLAKLTYTSAKLTILPEIILILGLAAVVVIDLLSKGK
NTFLLYKISMVTLLASAVILLWQWGFFTAYERSHARDFGNIFRFFLLICSSLSISSSVDY
ILCSKMSLAEFLLFKLAAGLGGMVLSCANDLVTIYVSLEFLALSSCFLSGYTKRDMRSNE
ATTKFLSMSGASSSPLLYGFSSLYGPSGGQLQLDKIVDGIIFNRYGSIIYLSAAFTTAGT
AFKLSLFPFHQWTPDVYEG
However, the amino acid sequence actually embedded in the feature
table looks like this:
/translation="MNDINLFLAKLTYTSAKLTILPEIILILGLVAVVVIDLLSKGKN
TFLLYKISMVTLLASAVILLWQWGFFTAYERSHARDFGNIFRFFLLICSLLSISSSVD
YILCSKMSLAEFLLFKLAAGLGGMVLSCANDLVTIYVSLEFLALSSCFLSGYTKRDMR
SNEATMKFLLMSGASSSLLLYGFSLLYGLSGGQLQLDKIVDGIIFNRYGSIIYLSAAF
TTAGTAFKLSLFPFHQWTPDVYEGSPTPVVAFFSVTSKVAALALFTRLFGLIFPYFSN
EWHVAVGLLATFSMILGNLIAVTQRSVKRMLAFSSISQIGYIMIGVLSADSGNGYASM
ITYTFIYILMNLGTFACITLFGLRTGTDNIRDYAGLYMKDPVLTFSLVLCLLSLGGMP
PLSGFFGKLYLFWHGWKAGLYSLVLVALVTSVISIYYYLKIIKLMFTGKSGRSDTPLN
SRQNSLVSLSISISKNSLEIAMIICALASTLSGIFIDPIIEITRNTFF"
as you can see they are clearly different, with the first even having
a "plus" sign embedded in it. If anyone could give any insight into
this problem I would appreciate it.
I'm not certain if it is related or not, but the Refseq version of
the same genome:
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi??
db=nucleotide&val=NC_004766
does not even open correctly in Artemis v8. The raw sequences seems
to load, but no features.
Thanks in advance for your help,
Cedar Mckay
University of Washington
Oceanography
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