I cannot see how the translation in that entry is arrived at. It seems as if their exons appear to be translated in a different order to the way it appears in artemis. At a guess, is it to do with it being circular?
The refseq entry can be read in if you remove the ‘PROJECT’ line which artemis does not like (I will fix this for the next release).
Regards
Tim
From: [EMAIL PROTECTED]
Date: 10 March 2006 23:35:41 GMT
To: [email protected]
Subject: [Artemis-users] NCBI files, incorrect peptide sequence
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
_______________________________________________
Artemis-users mailing list
[email protected]
http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
_______________________________________________ Artemis-users mailing list [email protected] http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
