index.php from eXtensible Genome Data Broker at Krugle

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<?php
if(empty($SITEDEF_H)){require('SITEDEF.php');}
if(empty($PARAM_H)){require('getPARAM.php');}
require('SSI_GDBprep.php');
virtual("${CGIPATH}SSI_GDBgui.pl/TWO_COLUMN_HEADER/" . $SSI_QUERYSTRING);
?>

<div id='mainWLS' align="center">

<CENTER>
<TABLE>
<TR><TD><A HREF="http://www.plantgdb.org/cgi-bin/PlantGDB/GeneSeqer/PlantGDBgs.cgi"><IMG SRC="sleuth1.JPG" WIDTH=101 HEIGHT=121 ALIGN=left></A>
</TD><TD align='center'><P><FONT SIZE="+3" COLOR="#009900"><B>AtGDB Gene Structure Annotation: HOW-TO</B></FONT><BR>
a tutorial for classroom and individual use<BR>
developed in collaboration with Ames, Iowa, area high schools<BR><BR>
( Special thanks to Mr. Michael Lawler of Nevada High School )
</P></TD>
</TABLE>
</CENTER>

<P><FONT SIZE="+1">
PlantGDB is a project at Iowa State University funded by the National Science Foundation.
The project involves staff and students in the group of bioinformatics professor
</FONT><A HREF="http://gremlin1.zool.iastate.edu/~volker/" TARGET="_blank"><FONT SIZE="+1">Dr. Volker Brendel</FONT></A><FONT SIZE="+1">
and seeks to provide resources, tools, and analyses for plant comparative genomics.
A key part of our work is to annotate plant genomes and in particular to find all the protein coding genes in the genome.
It turns out, YOU can help with this!
This site is designed to teach you both the biological background and the step-by-step procedures of gene structure annotation.
If you are a high school teacher, this site might provide a module for your classroom.
If you are a student, you could begin your studies right here and now - all you will need is provided via web tools.
Please contact <A HREF="mailto:vbrendel@iastate.edu">us</A> with questions and suggestions.
</FONT>
</P>

<P>&nbsp;</P>

<CENTER><FONT SIZE="+2" COLOR="#00CC00"><U>FIRST THINGS FIRST</U></FONT></CENTER>

<P><FONT SIZE="+1">In order to understand what we'll be doing, it is
first necessary to understand a few basic </FONT>
<A HREF="terms_and_concepts.htm" TARGET="_blank"><FONT SIZE="+1">concepts and vocabulary terms</FONT></A>
<FONT SIZE="+1">. Please click</FONT>
<A HREF="terms_and_concepts.htm" TARGET="_blank"><FONT SIZE="+1">here</FONT></A>
<FONT SIZE="+1">to look through the list of relevant vocabulary terms and visit some
of the excellent informational sites also listed on this page.</FONT></P>

<HR>

<CENTER><FONT SIZE="+2" COLOR="#00CC00"><U>EXPLANATION</U></FONT></CENTER>

<P><FONT SIZE="+1">Simply put, we'll be comparing a sequence of DNA
with all previously sequenced strands of DNA and RNA to see if there are any
matches, or correlations, and to see how many, if any, genes may be
located within the sequence. The reasons for doing this are many
fold. The information gleaned from this process can be used a number
of ways, all of which will advance our collective understanding of
biotechnology and genetics.</FONT></P>

<P><FONT SIZE="+1">Shortly, you will be entering a sequence of
DNA&nbsp;from a selected list into a program called "GeneSeqer"
(</FONT><A HREF="http://bioinformatics.iastate.edu/bioinformatics2go/gs/help.html" TARGET="_blank"><FONT SIZE="+1">What is GeneSeqer?</FONT></A><FONT SIZE="+1">). When you submit this
sequence, it will be compared to sequences stored at the national database
(</FONT><A HREF="http://www.ncbi.nlm.nih.gov/Genbank/GenbankOverview.html" TARGET="_blank"><FONT SIZE="+1">GenBank</FONT></A><FONT SIZE="+1">)
where all previously recorded biological sequences (DNA,RNA,and protein) are stored. What you
get back from this submission will be all of the DNA&nbsp;sequences
in GenBank that match your sequence along with their description,
where they came from, and who worked with them. You can then compare
these sequences with your sequence to see which organisms match and
possibly what the functions of the matching sequences are. The output
is also very helpful in discerning where actual genes may be located
on your DNA&nbsp;sequence.</FONT></P>

<P>&nbsp;</P>

<CENTER><FONT SIZE="+1" COLOR="#000066">When you feel you are
familiar with the vocabulary and are ready to begin, please click the
enter button.</FONT>

<P><A HREF="walkthrough.php"><IMG SRC="fenter.jpg" ALT="START" WIDTH=89 HEIGHT=32 ALIGN=middle></A></P></CENTER>
</div>

<?php
require('SSI_GDBprep.php');
virtual("${CGIPATH}SSI_GDBgui.pl/STANDARD_FOOTER/" . $SSI_QUERYSTRING);
?>

See more files for this project here

eXtensible Genome Data Broker

The xGDB project provides scientists with an online portal for the integration of diverse sources of genomic data. Portals allow researchers to effectively target a specific scientific question by customizing their interactions with available data.

Project homepage: http://sourceforge.net/projects/xgdb
Programming language(s): JavaScript,Perl,PHP
License: other

  GeneSeqerTutorial_files/
    AtGDB_logo.png
    BGlogo.jpg
    GSQdisplay.png
    PSI.gif
    PlantGDB.gif
    SBdetailedGSQ.png
    SBprotGSQ.png
    Thumbs.db
    image001.gif
    isu.gif
    nsflogo.gif
    pgdb.gif
    validate.js
  Exon_Intron.2.jpg
  Exon_Intron.JPG
  GeneSeqerTutorial.htm
  NCBI.logo.gif
  SBdetailedGSQ.png
  SBprotGSQ.png
  VolkerGroup.logo.jpg
  ZmDB.Logo.jpg
  fenter.jpg
  home.jpg
  index.php
  interpreting_results.htm
  pgdb.plants.gif
  sleuth.gif
  sleuth1.JPG
  terms_and_concepts.htm
  transcription.gif
  transcription1.gif
  walkthrough.php