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<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#0000ff">What do I need to do, or have our IT guy adjust, to be able to grab sequences from ncbi (genbank, refseq, etc.) into my directory on a LINUX mainframe? This used
to work under GCG via net fetch. I'm using </font><span class="Apple-style-span" style="color: rgb(0, 0, 255); ">EMBOSS 6.6.0.0, command line.</span></div>
<div style="font-family: Calibri, sans-serif; "><span class="Apple-style-span" style="color: rgb(0, 0, 255); "><br>
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<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#0000ff">I can use seqret to grab embl sequences (seqret embl:accession) and that works fine, however none of the synonyms that I can think of for genbank work.</font></div>
<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#0000ff"><br>
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<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#0000ff">Should our system have access through drcat? I do see Genbank, and many other remotes listed there. I'm not sure how that works.</font></div>
<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#0000ff"><br>
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<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#0000ff">I'm also not sure why it accesses embl sequences because embl isn't listed by showdb.</font></div>
<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#0000ff"><br>
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<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#0000ff">showdb produces:</font></div>
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<div style="color: rgb(0, 0, 255); "><font class="Apple-style-span" face="Courier">Display information on configured databases</font></div>
<div style="color: rgb(0, 0, 255); "><font class="Apple-style-span" face="Courier"># Name Type Comment</font></div>
<div style="color: rgb(0, 0, 255); "><font class="Apple-style-span" face="Courier"># ============= ======== =======</font></div>
<div style="color: rgb(0, 0, 255); "><font class="Apple-style-span" face="Courier">taxon Taxonomy NCBI taxonomy</font></div>
<div style="color: rgb(0, 0, 255); "><font class="Apple-style-span" face="Courier">drcat Resource Data Resource Catalogue</font></div>
<div style="color: rgb(0, 0, 255); "><font class="Apple-style-span" face="Courier">chebi Obo Chemical Entities of Biological Interest</font></div>
<div style="color: rgb(0, 0, 255); "><font class="Apple-style-span" face="Courier">eco Obo Evidence code ontology</font></div>
<div style="color: rgb(0, 0, 255); "><font class="Apple-style-span" face="Courier">edam Obo EMBRACE Data and Methods ontology</font></div>
<div style="color: rgb(0, 0, 255); "><font class="Apple-style-span" face="Courier">edam_data Obo EMBRACE Data and Methods ontology (data)</font></div>
<div style="color: rgb(0, 0, 255); "><font class="Apple-style-span" face="Courier">edam_format Obo EMBRACE Data and Methods ontology (formats)</font></div>
<div style="color: rgb(0, 0, 255); "><font class="Apple-style-span" face="Courier">edam_identifier Obo EMBRACE Data and Methods ontology (identifiers)</font></div>
<div style="color: rgb(0, 0, 255); "><font class="Apple-style-span" face="Courier">edam_operation Obo EMBRACE Data and Methods ontology (operations)</font></div>
<div style="color: rgb(0, 0, 255); "><font class="Apple-style-span" face="Courier">edam_topic Obo EMBRACE Data and Methods ontology (topics)</font></div>
<div style="color: rgb(0, 0, 255); "><font class="Apple-style-span" face="Courier">go Obo Gene Ontology</font></div>
<div style="color: rgb(0, 0, 255); "><font class="Apple-style-span" face="Courier">go_component Obo Gene Ontology (cellular components)</font></div>
<div style="color: rgb(0, 0, 255); "><font class="Apple-style-span" face="Courier">go_function Obo Gene Ontology (molecular functions)</font></div>
<div style="color: rgb(0, 0, 255); "><font class="Apple-style-span" face="Courier">go_process Obo Gene Ontology (biological processes)</font></div>
<div style="color: rgb(0, 0, 255); "><font class="Apple-style-span" face="Courier">pw Obo Pathways ontology</font></div>
<div style="color: rgb(0, 0, 255); "><font class="Apple-style-span" face="Courier">ro Obo Relations ontology</font></div>
<div style="color: rgb(0, 0, 255); "><font class="Apple-style-span" face="Courier">so Obo Sequence ontology</font></div>
<div style="color: rgb(0, 0, 255); "><font class="Apple-style-span" face="Courier">swo Obo Software ontology</font></div>
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<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#ffffff"># Name Type Comment</font></div>
<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#ffffff"># ============= ======== =======</font></div>
<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#ffffff">taxon Taxonomy NCBI taxonomy</font></div>
<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#ffffff">drcat Resource Data Resource Catalogue</font></div>
<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#ffffff">chebi Obo Chemical Entities of Biological Interest</font></div>
<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#ffffff">eco Obo Evidence code ontology</font></div>
<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#ffffff">edam Obo EMBRACE Data and Methods ontology</font></div>
<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#ffffff">edam_data Obo EMBRACE Data and Methods ontology (data)</font></div>
<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#ffffff">edam_format Obo EMBRACE Data and Methods ontology (formats)</font></div>
<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#ffffff">edam_identifier Obo EMBRACE Data and Methods ontology (identifiers)</font></div>
<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#ffffff">edam_operation Obo EMBRACE Data and Methods ontology (operations)</font></div>
<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#ffffff">edam_topic Obo EMBRACE Data and Methods ontology (topics)</font></div>
<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#ffffff">go Obo Gene Ontology</font></div>
<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#ffffff">go_component Obo Gene Ontology (cellular components)</font></div>
<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#ffffff">go_function Obo Gene Ontology (molecular functions)</font></div>
<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#ffffff">go_process Obo Gene Ontology (biological processes)</font></div>
<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#ffffff">pw Obo Pathways ontology</font></div>
<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#ffffff">ro Obo Relations ontology</font></div>
<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#ffffff">so Obo Sequence ontology</font></div>
<div style="font-family: Calibri, sans-serif; "><font class="Apple-style-span" color="#ffffff">swo Obo Software ontology</font></div>
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