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mirror.pl Posted by naveen (naveen), 28 January 2008 can anyone help me out wit downloading or copying a ncbi file using a program.i read about mirror.pl.but cant understand it.Posted by KevinAD (KevinAD), 28 January 2008 Typically you can use LWP::Simple to get pages/files from the internet. What is an ncbi file? Posted by admin (Graham Ellis), 29 January 2008 I think an ncbi file is a bioinformatics format - similar to FastA? But, please Naveen, do post a little bit more detail of your question as you've not given us very many pointers. Please bear in mind that we're very much advisors on helping with programs that you are writing where you come across coding problems, rather than being able to help with what could be larger programs written by others. Post 10 or 20 lines of code and say "why can't I get this to work - I've tried X and Y" and we're in our element. But you'll get far better advise about someone else's code by getting in touch with the people who wrote it (which you should find in the code or documentation) or support forums they and their friends have set up for the specific code if it's popular. Posted by naveen (naveen), 31 January 2008 this is an ncbi file which i was referring toLOCUS ZP_01386825 252 aa linear BCT 20-JUL-2006 DEFINITION PAS [Chlorobium ferrooxidans DSM 13031]. ACCESSION ZP_01386825 VERSION ZP_01386825.1 GI:110598556 DBSOURCE REFSEQ: accession NZ_AASE01000022.1 KEYWORDS . SOURCE Chlorobium ferrooxidans DSM 13031 ORGANISM Chlorobium ferrooxidans DSM 13031 Bacteria; Chlorobi; Chlorobia; Chlorobiales; Chlorobiaceae; Chlorobium/Pelodictyon group; Chlorobium. REFERENCE 1 (residues 1 to 252) AUTHORS Copeland,A., Lucas,S., Lapidus,A., Barry,K., Glavina del Rio,T., Dalin,E., Tice,H., Bruce,D., Pitluck,S. and Richardson,P. CONSRTM US DOE Joint Genome Institute (JGI-PGF) TITLE Sequencing of the draft genome and assembly of Chlorobium ferroxidans DSM 13031 JOURNAL Unpublished REFERENCE 2 (residues 1 to 252) AUTHORS Larimer,F., Land,M. and Hauser,L. CONSRTM US DOE Joint Genome Institute (JGI-ORNL) TITLE Annotation of the draft genome assembly of Chlorobium ferroxidans DSM 13031 JOURNAL Unpublished REFERENCE 3 (residues 1 to 252) AUTHORS Copeland,A., Lucas,S., Lapidus,A., Barry,K., Glavina del Rio,T., Dalin,E., Tice,H., Bruce,D., Pitluck,S. and Richardson,P. CONSRTM US DOE Joint Genome Institute (JGI-PGF) TITLE Direct Submission JOURNAL Submitted (11-JUL-2006) US DOE Joint Genome Institute, 2800 Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA COMMENT PREDICTED REFSEQ: The mRNA record is supported by experimental evidence; however, the coding sequence is predicted. The reference sequence was derived from EAT58366. URL -- http://www.jgi.doe.gov JGI Project ID: 4001304 Source DNA and Bacteria available from Don Bryant (dab14@psu.edu) Bacteria also available from DSMZ: DSM 13031 Contacts: Don Bryant (dab14@psu.edu) Paul Richardson (microbes@cuba.jgi-psf.org) Whole genome sequencing and draft assembly at JGI-PGF Annotation by JGI-ORNL The JGI and collaborators endorse the principles for the distribution and use of large scale sequencing data adopted by the larger genome sequencing community and urge users of this data to follow them. It is our intention to publish the work of this project in a timely fashion and we welcome collaborative interaction on the project and analysis. (http://www.genome.gov/page.cfm?pageID=10506376). Method: conceptual translation. FEATURES Location/Qualifiers source 1..252 /organism="Chlorobium ferrooxidans DSM 13031" /strain="DSM 13031" /db_xref="taxon:377431" Protein 1..252 /product="PAS" /calculated_mol_wt=28517 Region 23..110 /region_name="PAS" /note="PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels; cd00130" /db_xref="CDD:29035" Region <29..>214 /region_name="PRK09776" /note="predicted diguanylate cyclase, GGDEF domain signaling protein; PRK09776" /db_xref="CDD:77397" Site order(39,43,49,62..65,90,95) /site_type="other" /note="putative active site" /db_xref="CDD:29035" Site order(59,63,71,74..75,102,104) /site_type="other" /note="heme pocket" /db_xref="CDD:29035" Region 152..230 /region_name="PAS" /note="PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels; cd00130" /db_xref="CDD:29035" Site order(156,160,166,179..182,207,212) /site_type="other" /note="putative active site" /db_xref="CDD:29035" Site order(176,180,188,190..191,219,221) /site_type="other" /note="heme pocket" /db_xref="CDD:29035" CDS 1..252 /locus_tag="CferDRAFT_0414" /coded_by="NZ_AASE01000022.1:31939..32697" /note="PFAM: PAS" /transl_table=11 /db_xref="InterPro:IPR000014" ORIGIN 1 mitqgkniqq qaeqdpdrff dlipdpvciv ssdgsfrkvn aawelvlgys neellsisff 61 dlihpedrel tikelepqaa lknrhfinry raksgdyrwl ewnanpadgg vlyatardvt 121 crieaeeqir lladtftwca hgiaigipst krimtcnhaf aamhgmside vsgqlffdly 181 pesehaaiqr hltelkqkds lrfetrrlkk dgsvfaaqmd ivniqddqgq galsyhnssg 241 yhrknkargc tp // if i have to use this file, it has to be in my computer so that i can specify the path in the perl program. i m askin how should i get this file directly to my computer without copyin it. is there any perl code for this. Posted by KevinAD (KevinAD), 31 January 2008 There is no way to get it into your computer without copying it. For your perl program to be able to use the file you will have to store a copy of it to disk or memory in your computer. How you get the file depends on where it is. Unless we know where it is so we can't really provide specific information about how you can get it.This page is a thread posted to the opentalk forum
at www.opentalk.org.uk and
archived here for reference. To jump to the archive index please
follow this link.
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