<div dir="ltr">There's some sample code in the BioJava cookbook: <a href="https://github.com/biojava/biojava-tutorial/blob/master/genomics/genebank.md">https://github.com/biojava/biojava-tutorial/blob/master/genomics/genebank.md</a><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Jul 14, 2015 at 7:11 PM, Spencer Bliven <span dir="ltr"><<a href="mailto:sbliven@ucsd.edu" target="_blank">sbliven@ucsd.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div><div>Markus,<br><br></div>Good to hear from you! Are you still developing scabio for your class?<br><br></div>There has been a lot of GenBank work recently, so make sure you're using 4.1.0. There are definitely reader and writer classes. They should take an InputStream if you open an http stream. There's also a GenbankProxySequenceReader which can fetch from NCBI.<br><br></div>You can also post questions like this to <a href="mailto:biojava-l@lists.open-bio.org" target="_blank">biojava-l@lists.open-bio.org</a>.<br><br></div>Cheers,<br></div>Spencer<br></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jul 10, 2015 at 5:22 PM, Markus Gumbel <span dir="ltr"><<a href="mailto:m.gumbel@hs-mannheim.de" target="_blank">m.gumbel@hs-mannheim.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div link="#0563C1" vlink="#954F72" lang="DE"><div><p class="MsoNormal"><span lang="EN-US">Dear Spencer,<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p><p class="MsoNormal"><span lang="EN-US">I hope you remember me: We once met in Berlin and you contributed to the scabio repository. Now I have question: Is it possible with biojava4 (or 3) to access Genbank sequences directly over the web? I haven’t found any suitable classes in the javadocs and even Google isn’t very informative. Thanks for you answer!<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p><p class="MsoNormal"><span lang="EN-US">Best,<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p><p class="MsoNormal"><span lang="EN-US">Markus<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p><div style="border:none;border-bottom:solid windowtext 1.0pt;padding:0cm 0cm 5.0pt 0cm"><p class="MsoNormal" style="border:none;padding:0cm"><span style="font-size:9.0pt" lang="EN-US"><u></u> <u></u></span></p></div><p class="MsoNormal"><span style="font-size:9.0pt" lang="EN-US">Dr. Markus Gumbel, Professor Medical Informatics / Foreign Student Advisor at the Department of Computer Science</span><span style="font-size:9.0pt" lang="EN-US"><u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:9.0pt" lang="EN-US">Mannheim University of Applied Sciences, Department of Computer Science/Institute f. Medical Informatics</span><span style="font-size:9.0pt" lang="EN-US"><u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:9.0pt">Paul-Wittsack-Straße 10, D-68163 Mannheim, Germany</span><span style="font-size:9.0pt"><u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:9.0pt" lang="EN-US">Phone: <a href="tel:%2B49%20621%20292-6246" value="+496212926246" target="_blank">+49 621 292-6246</a>,</span><span style="font-size:9.0pt" lang="EN-US"> </span><span style="font-size:9.0pt"><a href="http://mi.informatik.hs-mannheim.de/gumbel/en" target="_blank"><span style="color:blue" lang="EN-US">http://mi.informatik.hs-mannheim.de/gumbel/en</span></a></span><span style="font-size:9.0pt"> </span><span style="font-size:9.0pt" lang="EN-US"><u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:9.0pt" lang="EN-US"> </span><span style="font-size:9.0pt" lang="EN-US"><u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:8.0pt;color:#a6a6a6">Haftungsausschluss:</span><span style="font-size:8.0pt;color:#a6a6a6"><u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:8.0pt;color:#a6a6a6">Die in dieser E-Mail und den dazugehörigen Anhängen (zusammen die "Nachricht") enthaltenen Informationen sind nur fuer den Adressaten bestimmt und können vertrauliche oder rechtlich geschützte Informationen enthalten. Sollten Sie die Nachricht irrtuemlich erhalten haben, löschen Sie die Nachricht bitte und benachrichtigen Sie den Absender. Die unbefugte Weitergabe, das Anfertigen von Kopien und jede Veränderung der E-Mail ist untersagt. Wir schließen jegliche Haftung fuer Verluste oder Schäden aus, die durch Inhalte veränderter Nachrichten oder virenbefallene Software verursacht werden.</span><span style="font-size:8.0pt;color:#a6a6a6"><u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:8.0pt;color:#a6a6a6"> </span><span style="font-size:8.0pt;color:#a6a6a6"><u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:8.0pt;color:#a6a6a6" lang="EN-US">Disclaimer:</span><span style="font-size:8.0pt;color:#a6a6a6" lang="EN-US"><u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:8.0pt;color:#a6a6a6" lang="EN-US">The information contained in this e-mail and any attachments (together the "message") is intended for the addressee only and may contain confidential or privileged information. If you have received the message by mistake please delete it and notify the sender. The unauthorized dissemination, copying and change of this e-mail are strictly forbidden. We accept no liability for any loss or damage caused by changes of the original message or software viruses.</span><span style="font-size:8.0pt;color:#a6a6a6" lang="EN-US"><u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p></div></div></blockquote></div><br></div>
</div></div></blockquote></div><br></div>