Thanks, Julian, Artemis or ACT are able to ignore such mesges, but anmother probem is that it show another rorr mesage " failed to open NC_002655.gbk: sequence file contains a character that is not a letter: 1 at line: 123959 " In this particular case, after clicking "OK" I get " source can't have mol_type as a qualifier gene can't have locus_tag as a qualifier CDS can't have selenocysteine as a qualifier " That line, most probably, represnts the the first row whre the nucleotide sequence starts. It does this not only with this particular sequence but aso with others. I have never had ths prblem with NCBI sequecnes dowloaded one or two years ago - this is an observation only.
Thank you Leka ----- Original Message ----- From: "Julian Parkhill" <[EMAIL PROTECTED]> To: "lekap@" <[EMAIL PROTECTED]> Cc: "ARTEMIS_USER" <[EMAIL PROTECTED]> Sent: Wednesday, April 28, 2004 5:06 AM Subject: Re: [artemis-users] ARTEMIS/ACT reading "mol_type as a qualifier" "locus_tag as a qualifier " > Leka, > > I believe these are only warnings; they should not prevent Artemis opening the > file. Artemis keeps an internal list of what qualifiers are allowed for what > keys in EMBL/GenBank (although it appears to be out of date, as these should be > legitimate). If it finds a qualifier it thinks is wrong, it will give a warning, > but it should not fail. These warnings can be suppressed by including the > qualifiers in the options file, under "extra qualifiers" (see > http://www.sanger.ac.uk/Software/Artemis/v5/manual/options-descriptions.html). > > If Artemis is failing to open the file, there are likely to be other reasons. > > Julian. > > "lekap@" wrote: > > > > Hi there > > > > I am having a [serious] problem recently when loading GenBank formatted > > files onto Artemis or ACT. > > > > I get the following message: > > " > > source can't have mol_type as a qualifier > > gene can't have locus_tag as a qualifier > > " > > > > Is there any way around it? > > > > Thank you > > > > Leka Papazisi > > > > Leka Papazisi, DVM PhD, > > Pathogen Functional Genomics > > Resource Center (PFGRC), > > The Institute for Genomic Research (TIGR), > > 9712 Medical Center Drive > > Rockville, MD 20850 > > 301-795-7583 Phone > > 301-838-0208 Fax > > http://pfgrc.tigr.org/ > > e-mail: [EMAIL PROTECTED] > > -- > Julian Parkhill > Senior Investigator, The Sanger Institute, > Wellcome Trust Genome Campus, > Hinxton, Cambridge, CB10 1SA, UK > > Visiting Professor in Microbial Genomics, > University of Oxford > > Tel: +44(0)1223 494975, Fax: +44(0)1223 494919 > http://www.sanger.ac.uk/Projects/Microbes > http://www.sanger.ac.uk/Teams/faculty/parkhill >
