index.php from eXtensible Genome Data Broker at Krugle

Show index.php syntax highlighted

<?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);
?>

<STYLE TYPE="text/css">

.breakout {color:#336666; font:bold 150% stencil,cursive;}
.ref {font:small-caps 100% monospace;}
.super {vertical-align:super; font:normal 0.5em monotype;}
.footnote {font:normal 0.75em monotype;}

H1 {color:#336666; text-align:center;}
  H1 IMG {padding:2px; border:1px dashed red;}
  H1 SPAN.breakout {color:#33FF33; text-decoration:underline;}

TABLE#flag_table {border:1px solid maroon;}
  TABLE#flag_table IMG {padding:2px; border:1px solid grey;}

DIV#methods {text-align:justify;}
  DIV#methods H3 {padding:1px 5px; border:1px solid maroon; margin-right:50%; margin-bottom:2px; background:#336666; color:#FFFFFF; font:bold 100% stencil,cursive;}
  DIV#methods P.synopsis {margin-top:2px; margin-left:25px;}

DIV#sidebar_locus {float:right; margin:5px -1px 2px 5px; width:49%; border:2px solid #336666; background:#CCCC99;}
  DIV#sidebar_locus H3 {text-align:center; padding:5px; margin:0px 0px 2px 0px; background:#999966; color:#FFFFFF; font:bold 100% stencil,cursive;}
  DIV#sidebar_locus TABLE#score_table {text-align:center; padding:5px 25px; width:100%;}
  DIV#sidebar_locus TABLE#score_table TH {vertical-align:bottom;}

DIV#discussion {width:100%;}
  DIV#discussion H2 {clear:both; padding:2px; margin-left:25px; margin-bottom:2px; background:#999966; color:#336666; font:bold 1em sans-serif}
  DIV#discussion H2 A.list_cases {position:absolute; right:8%; font-size:75%;}
  DIV#discussion IMG {margin-right:4px; vertical-align:bottom; padding:2px; border:1px solid grey; background:#FFFFFF;}
  DIV#discussion IMG.inline {float:right; clear:right; vertical-align:text-top; margin:2px 10px; border:1px solid #336666;}
  DIV#discussion P {margin:10px 5px 15px 25px; text-align:justify;}
  DIV#discussion P.sub {margin-top:1.5em; clear:right;}
  DIV#discussion H4 {margin:5px 0px 2px 25px;}

</STYLE>

<DIV ID="mainWLS">

<H1><IMG SRC=<?php echo "'${IMAGEDIR}Flags/gaeval.png'"; ?>>
<SPAN CLASS="breakout">G</SPAN>enome <SPAN CLASS="breakout">A</SPAN>nnotation <SPAN CLASS="breakout">EVAL</SPAN>uation
<IMG SRC=<?php echo "'${IMAGEDIR}Flags/gaeval.png'"; ?>></H1>

<TABLE ALIGN='CENTER' ID='flag_table'><TR>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/gaeval_more.png'"; ?>></TD>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/ssOVLAP5.png'"; ?>></TD>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/osOVLAP5.png'"; ?>></TD>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/UTR5_add.png'"; ?>></TD>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/UTR5_check.png'"; ?>></TD>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/UTR5_minus.png'"; ?>></TD>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/UTR5_amb.png'"; ?>></TD>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/UTR5_none.png'"; ?>></TD>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/AnnCov0.png'"; ?>></TD>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/AnnCov1.png'"; ?>></TD>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/AnnCov2.png'"; ?>></TD>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/AnnCov3.png'"; ?>></TD>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/AnnCov4.png'"; ?>></TD>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/UTR3_none.png'"; ?>></TD>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/UTR3_amb.png'"; ?>></TD>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/UTR3_minus.png'"; ?>></TD>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/UTR3_check.png'"; ?>></TD>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/UTR3_add.png'"; ?>></TD>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/osOVLAP3.png'"; ?>></TD>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/ssOVLAP3.png'"; ?>></TD>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/AltStr.png'"; ?>></TD>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/MergeGene.png'"; ?>></TD>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/SplitGene.png'"; ?>></TD>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/ATTgene.png'"; ?>></TD>
<TD><IMG SRC=<?php echo "'${IMAGEDIR}Flags/gaeval_more.png'"; ?>></TD>
</TR></TABLE>

<DIV ID='abstract'>
<P>The goal of the <SPAN CLASS="breakout">gaeval</SPAN> project is to assign quality scores to gene 
 structure predictions and to note exceptional cases of incongruence of the annotation with experimental
 evidence. These scores can be used as a quick reference of the current accuracy
 of a given gene annotation and to prioritize the re-evaluation of incongruent gene predictions.
</P>
</DIV>

<DIV ID='sidebar_locus'>
<H3>Expressed Sequence Origin:<BR>Assesment and Assignment</H3>
<TABLE ID='score_table'>
<TR><TH>Score</TH><TH>Confirmation<SPAN CLASS='super'>1</SPAN></TH><TH>Congruence<SPAN CLASS='super'>2</SPAN></TH>
<TH>Containment<SPAN CLASS='super'>3</SPAN></TH><TH>Consistency<SPAN CLASS='super'>4</SPAN></TH></TR>
<TR><TD>16</TD><TD>+</TD><TD>+</TD><TD>+</TD><TD>+</TD></TR>
<TR><TD>15</TD><TD>+</TD><TD>+</TD><TD>+</TD><TD>-</TD></TR>
<TR><TD>14</TD><TD>+</TD><TD>+</TD><TD>-</TD><TD>+</TD></TR>
<TR><TD>13</TD><TD>+</TD><TD>+</TD><TD>-</TD><TD>-</TD></TR>
<TR><TD>12</TD><TD>+</TD><TD>-</TD><TD>+</TD><TD>+</TD></TR>
<TR><TD>11</TD><TD>+</TD><TD>-</TD><TD>+</TD><TD>-</TD></TR>
<TR><TD>10</TD><TD>+</TD><TD>-</TD><TD>-</TD><TD>+</TD></TR>
<TR><TD>9</TD><TD>+</TD><TD>-</TD><TD>-</TD><TD>-</TD></TR>
<TR><TD>8</TD><TD>-</TD><TD>+</TD><TD>+</TD><TD>+</TD></TR>
<TR><TD>7</TD><TD>-</TD><TD>+</TD><TD>+</TD><TD>-</TD></TR>
<TR><TD>6</TD><TD>-</TD><TD>+</TD><TD>-</TD><TD>+</TD></TR>
<TR><TD>5</TD><TD>-</TD><TD>+</TD><TD>-</TD><TD>-</TD></TR>
<TR><TD>4</TD><TD>-</TD><TD>-</TD><TD>+</TD><TD>+</TD></TR>
<TR><TD>3</TD><TD>-</TD><TD>-</TD><TD>+</TD><TD>-</TD></TR>
<TR><TD>2</TD><TD>-</TD><TD>-</TD><TD>-</TD><TD>+</TD></TR>
<TR><TD>1</TD><TD>-</TD><TD>-</TD><TD>-</TD><TD>-</TD></TR>
<TR><TD>0</TD><TD COLSPAN=4> No Overlap With Annotation</TD><TR>
</TABLE>
<OL CLASS='footnote'>
<LI>The expressed sequence spliced alignment confirms at least one splice site.</LI>
<LI>Annotated splice junctions are completely consistent with the expressed sequence spliced alignment.</LI>
<LI>The expressed sequence spliced alignment is completely contained within the annotation region.</LI>
<LI>The expressed sequence spliced alignment does not contain any non-annotated splice sites.</LI>
</OL>
</DIV>

<DIV ID='methods'>
<P>Evaluation of a gene prediction is achevied through comparison with known expressed sequences. This involves
 determination of the cognate locus (genomic origin) of the expressed sequences, correlating the sequences with a 
 specific transcriptional isoform, and evaluating each annotation for incongruence.<BR>

<H3>Finding the cognate locus</H3>
<P CLASS='synopsis'>Cognate loci were identified by spliced alignment of <I>Arabidopsis</I> EST and cDNA onto the <I>Arabidopsis</I>
 genome. The inherent quality of a cognate alignment is generally sufficient to distinguish it from alignment to
 homologous loci.<BR><BR>
Details of these alignments are described in part in the manuscript
 <SPAN CLASS='ref'>"Refined annotation of the <I>Arabidopsis thaliana</I> genome by complete EST mapping"
 [W. Zhu, S.D. Schlueter and V. Brendel (2003) Plant Physiol. 132: 469-484]</SPAN>
 (see also <A href=<?php echo "'${PRJPATH}ZSB03PP/'"; ?>>ZSB03PP</A> on the
<A href=<?php echo "'${PRJPATH}'"; ?>>AtGDB Projects page</A>).
</P>

<H3>Assignment of a specific isoform</H3>
<P CLASS='synopsis'>In many cases, assignment of an expressed sequence alignment to a specific gene annotation
 is trivial in that the alignment overlaps only a single annotation. However overlapping gene annotations, 
 alternative splicing, clone-paired ESTs, and expressed sequences overlapping multiple adjacent annotations
 complicate matters. With this in mind, a scoring routine was devised as described in the sidebar
 "Expressed Sequence Origin: Assessment and Assignment" to ascertain the best assignment of an expressed sequence
 to a gene annotation isoform.</P>

<H3>Looking for trouble</H3>
<P CLASS='synopsis'>Each gene prediction is now compared with its cognate, isoform-specific expressed sequence
 spliced alignments. This comparison determines support for predicted splice junctions, the extent of the annotation region, 
 presence of alternative splice junctions, and alignment incongruence. Each of these properties is then
 scored, flagged, and <A HREF='./gaeval_lists.php'>listed</A>. Methods for scoring and descriptions of each property are discussed below.</P>
</P>
</DIV>

<DIV ID='discussion'>
<H2><IMG SRC=<?php echo "'${IMAGEDIR}Flags/AltStr.png'"; ?>>Alternative Splicing
<A CLASS='list_cases' HREF='./gaeval_lists.php'>list cases</A></H2>
<P>
<IMG CLASS='inline' SRC='examples/altspl.png'>
Alternative splicing is determined through recognition of mutually exclusive
 incongruent exon designations (exon structures determined by spliced alignment
 which overlap annotated exons yet do not share common acceptor/donor boundaries).
</P>
<H4>Quality Scoring:</H4>
<P>These events are evaluated by the number of spliced alignments confirming
 an alternative structure summed over all structures alternative to the given
 annotation.
</P>

<H2><IMG SRC=<?php echo "'${IMAGEDIR}Flags/MergeGene.png'"; ?>>Gene Annotation Fusion
<A CLASS='list_cases' HREF='./gaeval_lists.php'>list cases</A></H2>
<P>
<IMG CLASS='inline' SRC='examples/fussion.png'>
Annotation Fusion is necessary when gene predictions are recognized as
 incorrectly splitting a single gene into multiple adjacent gene annotations. This
 is made apparent by alignment of overlapping ESTs, clone-paired ESTs, and 
 full-length cDNAs.
</P>
<H4>Quality Scoring:</H4>
<P>These events are scored by evaluating the overlap of the isoform-specific ESTs or cDNAs
 with respect to the individual annotations. A score is then assigned based on the
 percentage of each annotation accounted for by the isoform-specific ESTs or cDNAs.
</P>

<H2><IMG SRC=<?php echo "'${IMAGEDIR}Flags/SplitGene.png'"; ?>>Gene Annotation Fission
<A CLASS='list_cases' HREF='./gaeval_lists.php'>list cases</A></H2>
<P>
<IMG CLASS='inline' SRC='examples/fission.png'>
Annotation Fission is necessary when gene predictions are recognized as
 falsely merging multiple adjacent gene structures into a single gene annotation.
 This can be determined through non-overlapping alignments of full-length cDNAs
 and the evaluation of 3' EST clusters
 (see <A HREF='./cps.php'>a discussion of termination</A> for more details).
 Cases in this category include mistaken classifications of alternative
 transcriptional termination sites. However, measure has been taken to classify
 alternative termination events as such when reasonable evidence is available
 to warrant such classification (see below).
</P>
<H4>Quality Scoring:</H4>
<P>These events are scored based on the number of individually confirmed gene
 predictions determined to reside within the current annotation.
</P>

<H2><IMG SRC=<?php echo "'${IMAGEDIR}Flags/ATTgene.png'"; ?>>Alternative Transcript Termination Site
<A CLASS='list_cases' HREF='./gaeval_lists.php'>list cases</A></H2>
<P>
<IMG CLASS='inline' SRC='examples/att.png'>
Alternative transcriptional termination sites are often mistaken for incorrect
 gene annotation. Alternative termination may be a biologicaly relavent event and 
 is currently the topic of many studies. The alternative termination events flagged
 by gaeval correspond to annotations which match the criteria for fission yet would
 also show evidence of fusion should independent fission products be evaluated. In
 other words, if cDNA or 3' cluster evidence exists that a gene could be terminated
 at both its annotated terminus and a secondary terminus, it is placed in this category.
</P>
<H4>Quality Scoring:</H4>
<P>These events are scored relative to the maximum distance between any two hypothetical
 3' termini.
</P>

<H2><IMG SRC=<?php echo "'${IMAGEDIR}Flags/UTR5_amb.png'"; ?>><IMG SRC=<?php echo "'${IMAGEDIR}Flags/UTR3_amb.png'"; ?>>
Ambiguous Annotation Boundary 
<A CLASS='list_cases' HREF='./gaeval_lists.php'>list cases</A></H2>
<P>
<IMG CLASS='inline' SRC='examples/amb5.png'>
Annotations flagged with this property represent possible errors in gene structure
 determination caused by the automated gene structure annotation routines used for 
 <I>Arabidopsis</I> genome annotation. Specifically, this situation occurs when an
 EST or cDNA is aligned such that it may belong to either of two overlaping annotations.
 This most often occurs with ESTs or cDNAs which do not span a splice junction.
</P>
<H4>Quality Scoring:</H4>
<P>These events are not scored except for on a presence / absence basis.
</P>

<H2><IMG SRC=<?php echo "'${IMAGEDIR}Flags/UTR5_minus.png'"; ?>><IMG SRC=<?php echo "'${IMAGEDIR}Flags/UTR3_minus.png'"; ?>>
Unsupported 5' / 3' Extension of Gene Annotation (Overextended mRNA Predictions)
<A CLASS='list_cases' HREF='./gaeval_lists.php'>list cases</A></H2>
<P>
<IMG CLASS='inline' SRC='examples/ovext.png'>
Unsupported gene annotation boundaries are often the product of ab-initio gene
 prediction in concert with a lack of sequence evidence at the mRNA terminus. These
 cases are more often due to limited sequence information rather than inacurate gene
 annotation. This flag however provides an immediate cue as to the known extent of the
 UTR (UnTranslated Region) for a given annotation.
</P>
<H4>Quality Scoring:</H4>
<P>These events are ranked according to the size of the unsupported region.
</P>

<H2><IMG SRC=<?php echo "'${IMAGEDIR}Flags/UTR5_add.png'"; ?>><IMG SRC=<?php echo "'${IMAGEDIR}Flags/UTR3_add.png'"; ?>>
Supported 5' / 3' Extension of Gene Annotation (Underextended mRNA Predictions)
<A CLASS='list_cases' HREF='./gaeval_lists.php'>list cases</A></H2>
<P>
<IMG CLASS='inline' SRC='examples/unext.png'>
Underextended gene annotations represent gene predictions which do not make use of cognate,
 isoform-specific sequence alignments to determine the longest possible transcription unit.
</P>
<H4>Quality Scoring:</H4>
<P>These events are ranked according to the size of the region of extended support.
</P>

<H2><IMG SRC=<?php echo "'${IMAGEDIR}Flags/AnnCov0.png'"; ?>><IMG SRC=<?php echo "'${IMAGEDIR}Flags/AnnCov1.png'"; ?>>
<IMG SRC=<?php echo "'${IMAGEDIR}Flags/AnnCov2.png'"; ?>><IMG SRC=<?php echo "'${IMAGEDIR}Flags/AnnCov3.png'"; ?>>
<IMG SRC=<?php echo "'${IMAGEDIR}Flags/AnnCov4.png'"; ?>>
Credence Flags: Confidence in Predicted Gene Structure
<A CLASS='list_cases' HREF='#'>list cases</A></H2>
<P>The five pie-chart flags indicate degree of support for a gene structure prediction
 based on its similarity to cognate, isoform-specific sequence alignments.
</P>
<P CLASS='sub'>
<IMG CLASS='inline' SRC='examples/cov0.png'>
The first flag (empty pie) shows the least confirmed level of gene structure annotation in
 which no known expressed sequences have been assigned to this predicted gene and therefor
 no confirmation of splice donor / acceptor site positions is possible.
</P>
<P CLASS='sub'>
<IMG CLASS='inline' SRC='examples/cov1.png'>
The second flag (quarter pie) shows the next level of confirmation in which an expressed sequence
 exists in the region of the gene annotation, however no splice sites were confirmed by this /
 theses alignments. This level of confirmation implies the existence of a gene, yet tells little
 of its gene structure.
</P>
<P CLASS='sub'>
<IMG CLASS='inline' SRC='examples/cov2.png'>
The third flag (half pie) depicts a case of considerable improvement in confirmation of the
 given gene structure. These cases include annotations in which at least one splice site
 is confirmed by cognate spliced alignment.
</P>
<P CLASS='sub'>
<IMG CLASS='inline' SRC='examples/cov3.png'>
<IMG CLASS='inline' SRC='examples/cov4.png'>
The fourth and fifth flags (three-quarter and full pie) are reserved for annotations in which
 all splice sites are confirmed by sequence alignment. Three-quarter and full pie-chart
 annotations differ only in their sequence coverage. Three-quarter pie annotations include
 gaps in their aligned sequence coverage, whereas full pie annotations are completely covered
 from first exon to last.
</P>
</DIV>

</DIV>

<?php
require('SSI_GDBprep.php');
virtual("${CGIPATH}SSI_GDBgui.pl/STANDARD_FOOTER/" . $SSI_QUERYSTRING);
?>
See more files for this project here