From 17569085da45afd045f290cdf1d38d426525834b Mon Sep 17 00:00:00 2001
From: "J.F.J. Laros" <j.f.j.laros@lumc.nl>
Date: Fri, 14 Jan 2011 15:20:00 +0000
Subject: [PATCH] Added a FAQ and exercise page.
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@140 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
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templates/exercise.html | 377 ++++++++++++++++++++++++++++++++++++++++
templates/help.html | 2 +-
templates/menu.html | 16 ++
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+<html>
+ <head>
+ <link rel="stylesheet"
+ type="text/css"
+ href="base/css/style.css">
+ <title></title>
+ </head>
+ <body>
+ <div metal:define-macro="content">
+ <center>
+ <h3>Frequently Asked Questions</h3>
+ </center>
+
+ <h3>How should I refer to Mutalyzer? </h3>
+ <p>
+ Mutalyzer is described in:
+ </p>
+ <p>
+ Wildeman M, van Ophuizen E, den Dunnen JT, Taschner PE. Improving
+ sequence variant descriptions in mutation databases and literature using
+ the MUTALYZER sequence variation nomenclature checker.
+ <a href="http://www.ncbi.nlm.nih.gov/entrez/utils/fref.fcgi?PrId=3058&itool=AbstractPlus-def&uid=18000842&db=pubmed&url=http://dx.doi.org/10.1002/humu.20654">Hum Mutat 29:6-13 (2008)</a> [
+ <a href="http://www.ncbi.nlm.nih.gov/pubmed/18000842?">PMID:
+ 18000842</a>].
+ </p>
+
+ <h3>What does Mutalyzer do?</h3>
+ <p>
+ Mutalyzer checks sequence variant descriptions given a certain reference
+ sequence and, if necessary, tries to correct them according to the
+ <a href="http://www.hgvs.org/mutnomen/">HGVS nomenclature guidelines</a>.
+ Descriptions of its functionality can be found in the
+ <a href="help">Help file</a>.
+ </p>
+
+ <h3>Were can I find examples of Mutalyzer input data?</h3>
+ <p>
+ Most Mutalyzer web pages show an example of the input data accepted.
+ Additional descriptions of input data formats can be found in the
+ <a href="help">Help file</a>.
+ </p>
+
+ <h3>Can Mutalyzer analyze sequence traces?</h3>
+ <p>
+ No, Mutalyzer only checks sequence variant descriptions. Sequence
+ variant descriptions can be generated from sequence traces using third
+ party software, e.g., MutationSurveyor.
+ </p>
+
+ <h3>
+ Why does Mutalyzer only accept GenBank Accession Numbers or files in
+ GenBank format?
+ </h3>
+ <p>
+ Mutalyzer has been developed to extract sequence and annotation
+ information from files in GenBank format. This extraction of
+ information will not work properly with other formats.
+ </p>
+
+ <h3>
+ Why does Mutalyzer not work directly with GenBank Accession Numbers
+ starting with NC_ or NT_?
+ </h3>
+ <p>
+ GenBank Accession Numbers starting with NC_ or NT_ refer to contigs of
+ smaller sequences, potentially interspaced with gaps. Mutalyzer will
+ try to retrieve the underlying sequences to check the sequence variant,
+ but it may lose track of the corresponding positions due to the
+ different levels of assembly and return errors. Users are advised
+ circumvent this problem by using the Genbank uploader when (part of)
+ these NC_ or NT references are used. The
+ <a href="http://www.humgen.nl/mutalyzer_exercise.html">
+ Mutalyzer exercise</a> provides more detailed information.
+ </p>
+
+ <h3>
+ Why does Mutalyzer not accept positions outside exons when using a
+ coding DNA reference sequence?
+ </h3>
+ <p>
+ Mutalyzer uses the reference sequence to check for the presence of the
+ nucleotides at the positions specified. Since promoter sequences,
+ intron sequences and intergenic sequences are not included in a coding
+ DNA reference sequence, Mutalyzer is unable to check these and will
+ issue an "Out of bounds" error. We strongly suggest to use genomic
+ reference sequences to describe changes in promoter sequences, intron
+ sequences and intergenic sequences.
+ </p>
+
+ <h3>
+ I am using a genomic reference sequence, but I am still unable to check
+ intron variants
+ </h3>
+ <p>
+ Mutalyzer checks the annotation of the genomic reference sequence for
+ information about the genes, their exons and protein coding sequence.
+ When these features are not annotated, Mutalyzer is unable to use the
+ coding DNA numbering scheme and will return an error. Please note that
+ Mutalyzer ignores non-coding transcripts, because the coding DNA
+ numbering scheme can not be applied in the absence of a start codon.
+ The HGVS sequence variation nomenclature guidelines do not yet provide
+ guidance on this issue.
+ </p>
+
+ <h3>How do I find the correct reference sequence?</h3>
+ <p>
+ Although any file in GenBank format can be used, curated RefSeq
+ sequences are preferred (See
+ <a href="http://www.hgvs.org/mutnomen/refseq.html">HGVS Reference
+ Sequence discussion</a>). Most locus-specific mutation databases
+ (LSDBs) specify reference sequences for the genes of interest. In many
+ cases, these will be coding DNA reference sequences. If you want to
+ check changes in promoter sequences, intron sequences and intergenic
+ sequences, you should contact the curator of the LSDB to get a genomic
+ DNA reference sequence.
+ </p>
+ <p>
+ If you are the curator of an LSDB in need of an appropriate genomic
+ reference sequence, you can use the options on the GenBank uploader
+ page to select a genomic reference sequence. More information about the
+ selection and modification of reference sequences can be found in the
+ <a href="http://www.humgen.nl/mutalyzer_exercise.html">
+ Mutalyzer exercise</a>.
+ </p>
+
+ <h3>
+ I am using the correct RefSeq Accession number. Why is the position of
+ most or all sequence variants on transcript or protein level different
+ from what I expected?
+ </h3>
+ <p>
+ Every GenBank file has an Accession number and a version number (e.g.
+ AB026906.1). If the version number has not been specified, Mutalyzer
+ will use the last version of this file. The sequence annotation of the
+ last version may differ from that of an earlier version, leading to
+ new/changed transcripts and protein sequence information, which is
+ automatically used by Mutalyzer to describe the variants. Most
+ locus-specific mutation databases (LSDBs) specify the accession numbers
+ of reference sequences for the genes of interest, but they should also
+ include the version number to prevent unexpected Mutalyzer results. You
+ can check the influence of the version number on Mutalyzer's analysis
+ by specifying a previous version number. If this solves the problem,
+ please ask the curator of the LSDB to specify the correct version of
+ the reference sequence.
+ </p>
+
+ <h3>Why does Mutalyzer fail to recognize my SNP descriptions?</h3>
+ <p>
+ Mutalyzer checks if
+ <span style="font-size: 12pt; font-family: Times New Roman;">
+ the nucleotide changed is present in the reference sequence. SNPs are
+ commonly indicated in dbSNP as two or more possible alleles at the
+ same position of the sequence.
+ </span>
+ According to the HGVS nomenclature guidelines, only alleles which
+ differ from the reference can be described. As a result,
+ NM_003002.1:c.204C>T is approved, but NM_003002.1:c.204T>C will
+ result in an error. When the dbSNP identifier is known, the SNP
+ converter can be used to generate the correct description (see the
+ <a href="help">Help file</a> for more information.
+ </p>
+
+ <h3>
+ Why does the Genbank uploader not work with my local file or the URL
+ provided?
+ </h3>
+ <p>
+ Mutalyzer checks if it gets a
+ <span style="font-size: 12pt; font-family: Times New Roman;">
+ <a
+ href="http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html">GenBank
+ Flat file</a> in both cases. Other formats can not be processed
+ correctly and will generate an error.
+ </span>
+ </p>
+
+ <h3>
+ Why do large deletions seem shorter using coding DNA position numbering
+ than genomic position numbering?
+ </h3>
+ <p>
+ The difference in deletion size is caused by our intention to reflect
+ the effect of variations on transcript level, when coding DNA position
+ numbering is used. Therefore, ranges of deleted nucleotides are limited
+ to positions present in the coding DNA reference sequence.
+ </p>
+
+ <h3>
+ Can Mutalyzer analyze sequence variant descriptions from other
+ organisms?
+ </h3>
+ <p>
+ Yes, Mutalyzer can check sequence variant descriptions from other
+ organisms as long as a proper reference sequence is provided and the
+ HGVS sequence variation nomenclature guidelines are applied. Mutalyzer
+ will check the reference sequence annotation to determine which codon
+ table should be used for proper translation of coding sequences.
+ </p>
+
+ <h3>How do I create a batch checker file?</h3>
+ <p>
+ The easiest way to create a batch checker file is to download the
+ <a href="downloads/batchtestnew.txt">Example</a>
+ file. Please right-click the link and select "Save as" to download the
+ example file for modification. Open the batchtest.txt file in Excel.
+ The Text Import Wizard window will open to guide you through the import
+ procedure. Click "Finish" to finalize the import. The Excel spreadsheet
+ created should have three columns and a header row containing the
+ column names. You can add your data to the batchtest.txt file by typing
+ or pasting the required information into the appropriate fields. When
+ you are finished select "Save as" from the File menu and save your file
+ using a different name (without spaces!) as type: Text (tab
+ delimited)(*.txt).
+ </p>
+ <p>
+ In case of problems follow the separate import steps by verifying the
+ correct selections before clicking the "Next" button to go to step 2.
+ Click the "Next" button to go to step 3, click "Finish" to finalize the
+ import.
+ </p>
+
+ <h3>I am having trouble with the batch checker. What should I do?</h3>
+ <p>
+ The batch checker is relatively sensitive to unexpected file and file
+ name formats. Users are advised to check the following:
+ </p>
+ <p>
+ File name: The file name should not contain any spaces. Windows users
+ can check the file extension: if it is not .txt, but .doc or .xls, the
+ file is unlikely to be a tab-delimited textfile.
+ </p>
+ <p>
+ File format: The tab-delimited textfile should contain a header row
+ (the first line) containing the words
+ <b><i>AccNo Genesymbol Mutation</i></b> separated by a single tab.
+ </p>
+ <p>
+ File format: The file should be a tab-delimited text file. Excel users
+ can import the file to check its format. The file should have three
+ columns with the appropriate column names,
+ <b><i>AccNo Genesymbol Mutation</i></b>, respectively. The variant
+ information should be present in the corresponding columns.
+ </p>
+ <p>
+ The Genesymbol column/field may be left blank, when the reference
+ sequence contains only one gene, but a tab should be present. Please
+ note that Mutalyzer does not check the correctness of the gene symbol
+ in this case.
+ </p>
+
+ <h3>Why can't I use the bugtracker?</h3>
+ <p>
+ The bugtracker can only be accessed via a secure connection. Normally,
+ when you try to connect securely, sites will present trusted
+ identification to prove that you are going to the right place. However,
+ this site's identity can't be verified by the browser because the
+ security certificate is self signed (and not signed by the proper
+ authorities).<br>
+ A certificate that is signed by the proper authorities costs a lot of
+ money, so for the time being we have solved it in this way.<br>
+ To get access to the bugtracker, you need to add a security exception.
+ Usually the browser presents this option.
+ </p>
+ <p>
+
+ </p>
+ <hr>
+ <p>
+ If you have any comments or suggestions be sure to let us know!
+ </p>
+ <p>
+ Last modified: January 14, 2011
+ </p>
+ <a href="mailto:mutalyzer@humgen.nl"><address>mutalyzer@humgen.nl</address></a>
+ </div>
+ </body>
+</html>
diff --git a/templates/exercise.html b/templates/exercise.html
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--- /dev/null
+++ b/templates/exercise.html
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+<html>
+ <head>
+ <link rel="stylesheet"
+ type="text/css"
+ href="base/css/style.css">
+ <title></title>
+ </head>
+ <body>
+ <div metal:define-macro="content">
+ <center>
+ <h3>Sequence variation nomenclature checker demonstration</h3>
+ </center>
+
+ <h3>Checking sequence variation nomenclature</h3>
+ <p>
+ A few tools are available to check sequence variation nomenclature:
+ </p>
+ <ul>
+ <li>
+ <a href="http://mutation.sanbi.ac.za/checker">DNA Mutation Checker
+ 3</a> - Basic sequence variation check.<br> This basic mutation check
+ should be followed/supplemented by a sequence variation check
+ including splice site changes
+ </li>
+ <li>
+ <a href="index">Mutalyzer</a> - Sequence variation nomenclature
+ checker generating descriptions according to <a
+ href="http://www.hgvs.org/mutnomen/">HGVS nomenclature guidelines</a>
+ </li>
+ </ul>
+
+ <h3>Mutalyzer sequence variation nomenclature checker</h3>
+ <p>
+ <a href="index">The Mutalyzer sequence variation nomenclature
+ checker</a> has been developed as the first part of an integrated
+ modular package of tools, which should allow users to obtain
+ information about the effect of sequence variations in genes associated
+ with human disease. The <a href="index">Mutalyzer</a> package (under
+ development) should assist decision-making in molecular diagnosis based
+ on a sequence change detected in a patient's DNA and prevent
+ misdiagnosis caused by either missing the pathogenic effect of a
+ sequence variation reported as "polymorphic" or, more
+ seriously, reporting a polymorphic change as non-pathogenic.
+ </p>
+
+ <h3>Exercise</h3>
+ <p>
+ For this exercise, it is most convenient to right-click this
+ <a href="check">link</a> and open a separate window for Mutalyzer. The
+ exercise will demonstrate the use of the different functionalities of
+ the Mutalyzer sequence variation nomenclature checker. Its main
+ functions can be selected from the
+ <a href="index">index page</a> or the list on the left side of any
+ Mutalyzer window. For more information, please check this
+ <a href="help">help</a> file. Although the performance of Mutalyzer has
+ been checked using complete sequence variation database contents, some
+ changes might not be processed correctly. Please report any strange
+ results to <a href="mailto:mutalyzer@humgen.nl">mutalyzer@humgen.nl</a>
+ </p>
+
+ <h3>Selecting a reference file</h3>
+ <p>
+ Mutalyzer needs the annotation of a Genbank reference sequence file to
+ retrieve basic information for the check. Its functionality can be
+ appreciated best using well-annotated genomic reference sequences,
+ which contain information about all the transcripts and proteins
+ encoded by the reference sequence.
+ </p>
+ <p>
+ For many disease genes, LSDB curators should have specified a reference
+ sequence, preferably by listing its GenBank accession number. In many
+ cases, this will be a RefSeq record with an accession number starting
+ with NM_ (or XM_). These records describe transcript sequences and
+ cannot be used by Mutalyzer to describe intron variants. If you need to
+ check intron variants, please ask the LSDB curator to specify a
+ well-annotated genomic reference sequence. (See
+ <a href="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=Nucleotide&dopt=GenBank&val=16944057">AL449423.14</a> or NCBI's new
+ <a href="http://www.ncbi.nlm.nih.gov/RefSeq/RSG/">RefSeqGene</a>
+ records for example). Alternatively, you can use the GenBank Uploader
+ options described below to obtain a suitable genomic reference
+ sequence. If the annotation of this record contains information about
+ the transcript specified by the NM_ number, Mutalyzer can use the
+ genomic sequence record to describe any variant relative to this
+ transcript. Always use an Accession number (AL449423) in combination
+ with a specific version number (14). Otherwise, Mutalyzer automatically
+ uses the last version and may present unexpected results.
+ </p>
+ <p> </p>
+
+ <h3>
+ Before you start: Save
+ <a href="downloads/batchtestnew.txt">this tab-delimited text file</a>
+ to your Desktop and open it in WordPad.
+ </h3>
+
+ <p>
+ 1) The Mutalyzer Name Generator
+ </p>
+ <p>
+ The Mutalyzer Name Generator provides an easy check of a sequence
+ variation by returning the correct name of the variation according to
+ HGVS nomenclature guidelines with information about the sequence
+ surrounding the variation and the transcripts and proteins affected by
+ the variation. Mutalyzer accepts in principle any Genbank sequence as a
+ reference, but its functionality can be appreciated best using
+ well-annotated genomic reference sequences.
+ </p>
+ <p>
+ <i>Enter the accession number AL449423.14 as a reference sequence,
+ select "genomic DNA", enter start position "1", stop
+ position "1", select "deletion" and press
+ submit.</i>
+ </p>
+
+ <p>
+ The legend of the results describes the transcripts and proteins
+ annotated in the reference sequence.
+ </p>
+
+ <h3>
+ Add the description generated by Mutalyzer as a new line to the
+ tab-delimited text file. Make sure that the AccNo, Gene symbol and
+ description are separated by a single tab. Repeat this for all variants
+ in this part of the exercise.
+ </h3>
+ <p>
+ <i>On the Mutalyzer page, now select "coding DNA", enter one
+ of the gene symbols from the legend, and press submit to see the effect
+ of a change on the major transcript </i>(optional: enter, in addition
+ to the gene symbol, the number of a transcript variant, e.g., 2 or v002
+ for the second transcript annotated in the record)<i>.</i>
+ </p>
+ <p>
+ <i>Repeat this for the other gene symbols, additional sequence
+ variation types, changes in introns, across intron exon boundaries,
+ etc. </i>You may check the <a href="http://www.hgvs.org/mutnomen/">
+ HGVS nomenclature guidelines</a> or <a
+ href="http://www.hgvs.org/dblist/dblist.html">sequence variation
+ databases</a> for inspiration.
+ </p>
+ <p> </p>
+
+ <h3>
+ Save theWordPad file containing the sequence variation descriptions to
+ generate the text file for use with the batch checker in the third part
+ of the exercise.
+ </h3>
+ <p> </p>
+ <p>
+ 2) The Mutalyzer Name Checker
+ </p>
+ <p>
+ The Name Checker is most convenient when checking a few sequence
+ variations, which have been described in a putative correct format. The
+ description made by the generator can be submitted to the name checker
+ to regenerate the additional information. It also allows you to change
+ and check descriptions fast, once you get a feeling for it.
+ </p>
+ <p>
+ <i>Submit one of the descriptions generated by the Mutalyzer Name
+ Generator by pasting it into the submission box and pressing the submit
+ button.</i>
+ </p>
+ <p>
+ <i>Repeat this after changing the positions or nucleotide(s).</i>
+ </p>
+ <p>
+ Submit these descriptions to see the importance of a version number:
+ NM_000787.3:c.61A>G and NM_000787.2:c.61A>G.
+ </p>
+ <p>
+ Compare the CDS annotation of the corresponding files
+ <a href="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=116534899">NM_000787.3</a> and
+ <a href="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=18426905">
+ NM_000787.2</a> to see why Mutalyzer gives a different result.
+ </p>
+ <p>
+ How does NM_000787.3:c.61A>G compare to NM_000787.2:c.19A>G ?
+ </p>
+ <p> </p>
+ <p>
+ 3) The Mutalyzer SNP converter
+ </p>
+ <p>
+ The SNP converter has been developed to convert dbSNP identifiers to
+ HGVS compliant variant descriptions, based on the GenBank nucleotide
+ reference sequence specified by the user.
+ </p>
+ <p>
+ <i>Submit</i> rs9919552 <i>as SNP Accession number and</i> NM_003002
+ <i> as Nucleotide Accession number.</i>
+ </p>
+ <p>
+ <i>Open the UCSC Human Genome Browser in a new window to see additional
+ SNPs for this gene.</i>
+ </p>
+ <p> </p>
+ <p>
+ 4) The Mutalyzer sequence variation description batch checker
+ </p>
+ <p>
+ The batch checker has been developed for database curators, but can be
+ used with any list of sequence variations provided that they are
+ submitted in the correct format: a tab-delimited text file.
+ </p>
+ <p>
+ <i>Open the WordPad file containing the sequence variation descriptions
+ that you have checked before. </i>
+ </p>
+ <p>
+ <i>Duplicate some of the entries and create a few mistakes in
+ numbering, sequence type (e.g., replace duplication by insertion),
+ nucleotides, description format. </i>
+ </p>
+ <p>
+ <i>Submit the file together with your e-mail address (lower case only!)
+ to see the alerts and automatic corrections created by
+ Mutalyzer.</i>
+ </p>
+ <p> </p>
+ <p>
+ 4) The Mutalyzer reference sequence uploader
+ </p>
+ <p>
+ <span style="font-size: 12.0pt; font-family: Times New Roman">Users can
+ upload their own reference sequence file in GenBank format, retrieve
+ the genomic sequence of a gene with its flanking regions, or specify
+ a chromosomal range for use as a reference sequence. Mutalyzer checks
+ whether the file is in valid GenBank format. If so, Mutalyzer stores
+ the file locally for a limited time and returns a unique
+ <i> UD identifier</i> that can be used with all different forms of
+ the Mutalyzer Sequence Variation Nomenclature Checker, except the SNP
+ converter. This option allows users to use reference files, which are
+ not present in GenBank, or add information about alternative
+ transcripts or proteins or additional genes contained within or
+ derived from the reference sequence to an existing GenBank file. We
+ strongly recommend to limit your use of this option
+ </span>
+ and to send a request for a new RefSeqGene record to
+ <a href="mailto:rsgene@ncbi.nlm.nih.gov">rsgene@ncbi.nlm.nih.gov</a>.
+ <span style="font-size: 12.0pt; font-family: Times New Roman">
+ Alternatively, you can submit annotation updates and corrections of
+ existing GenBank files following <a style="color: blue;
+ text-decoration: underline; text-underline: single"
+ href="http://www.ncbi.nlm.nih.gov/Genbank/update.html">these
+ instructions</a>.
+ </span>
+ </p>
+ <p>
+ <i>
+ <span style="font-family: Times New Roman">Click the GenBank Uploader
+ link in
+ </span> the list on the left side of any Mutalyzer window to see its
+ options.
+ </i>
+ </p>
+ <p>
+ <span style="font-family: Times New Roman">
+ If you already have a well-annotated GenBank file on your computer or
+ stored on a web server, the first two GenBank uploader options
+ facilitate easy uploading and will return the
+ </span>
+ <span style="font-size: 12.0pt; font-family: Times New Roman">
+ unique <i>UD identifier</i>. This identifier can be used in the Name
+ generator or Name Checker, which will then provide a link to download
+ the record. This record can also be used as input for the LOVD
+ reference sequence parser.
+ </span>
+ </p>
+ <p>
+ <span style="font-size: 12.0pt; font-family: Times New Roman">
+ If you do not have
+ </span>
+ <span style="font-family: Times New Roman">
+ a well-annotated GenBank file, the last two options can provide one.
+ </span>
+ Curators of LOVD databases can use these options to generate
+ <span style="font-family: Times New Roman">
+ well-annotated
+ </span> genomic reference sequence files for import into LOVD2.0 using
+ the Reference Sequence Parser 2.0.
+ </p>
+ <p>
+ <span style="font-family: Times New Roman">
+ Option 3: Retrieving a well-annotated
+ </span>
+ genomic reference sequence file
+ <span style="font-family: Times New Roman">
+ using a (<a
+ href="http://www.genenames.org/guidelines.html">HGNC</a>-approved)
+ gene symbol in combination with the name of the organism (e.g. human,
+ mouse, etc.).
+ </span>
+ </p>
+ <p>
+ <span style="font-family: Times New Roman; font-style:italic">
+ Click the corresponding radio button and try this for your favourite
+ gene.
+ </span>
+ </p>
+
+ <p>
+ <span style="font-family: Times New Roman">
+ In some cases, this may not work for your gene due to ambiguous gene
+ symbols. If Mutalyzer mentions other problems, please report them! In
+ those cases, or when you would like to include additional flanking
+ sequences (e.g., promoters) you can also specify the range of a
+ chromosomal sequence using the fourth option. The easiest way to find
+ a chromosomal range is to search
+ <a
+ href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene">Entrez
+ Gene</a> using the gene symbol in combination with the name of the
+ organism.
+ </span>
+ </p>
+ <p>
+ <span style="font-family: Times New Roman">
+ <i>
+ Open <a
+ href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene">Entrez
+ Gene</a> in a new window and search with the gene symbol of your
+ favorite gene in combination with the name of the organism. Open
+ the correct link in the list of results and click on the link to
+ reference sequence details under the heading "Genomic regions,
+ transcripts and products".
+ </i>
+ </span>
+ </p>
+ <p>
+ <span style="font-family: Times New Roman">
+ Under the header "RefSeqs of Annotated Genomes", you will
+ find an Acc. No starting with NC_, which refers to a
+ chromosomal reference sequence. The positions behind Range refer to
+ the start of the most upstream exon and the end of the most
+ downstream exon, respectively.
+ </span>
+ </p>
+ <p>
+ <i>
+ Click on the Genbank link to view the sequence and its annotation.
+ You can save the file by changing "Send to" in the Entrez
+ menu bar to "Save".
+ </i>
+ </p>
+ <p>
+ <span style="font-family: Times New Roman">
+ Option 4: Retrieving a well-annotated
+ </span>
+ genomic reference sequence file
+ <span style="font-family: Times New Roman">
+ using chromosomal positions
+ </span>
+ </p>
+ <p>
+ <span style="font-family: Times New Roman; font-style:italic">
+ Click the corresponding radio button and
+ </span>
+ <i>
+ enter the NC_ Accession number and the range positions corresponding
+ to the gene of interest.
+ </i>
+ </p>
+ <p>
+ You can modify the (annotation of the) genomic reference sequence file
+ obtained via
+ <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene">Entrez
+ Gene</a>.using
+ <a href="http://www.ncbi.nlm.nih.gov/Sequin/netaware.html">Network
+ aware Sequin.</a>
+ </p>
+ <hr>
+ <p>
+ If you have any comments or suggestions, please let us know!<a href="mailto:mutalyzer@humgen.nl"><address>mutalyzer@humgen.nl</address></a>
+ </p>
+ </div>
+ </body>
+</html>
diff --git a/templates/help.html b/templates/help.html
index 62b9a28d..e879d3c5 100644
--- a/templates/help.html
+++ b/templates/help.html
@@ -946,7 +946,7 @@
<p>
Last modified: November 5, 2010
</p>
- <a href="mailto:Mutalyzer@humgen.nl">
+ <a href="mailto:mutalyzer@humgen.nl">
<address>mutalyzer@humgen.nl</address></a>
</div>
</body>
diff --git a/templates/menu.html b/templates/menu.html
index 0395641e..b7b7598a 100644
--- a/templates/menu.html
+++ b/templates/menu.html
@@ -324,6 +324,22 @@
</td>
</tr>
+ <tr>
+ <td valign="top" width="20">
+ <img src="base/images/bullitdonker.gif" id="b_faq">
+ </td>
+ <td colspan="3">
+ <a id="page_faq"
+ onclick="swapActive('faq');"
+ href="faq"
+ onmouseover="navAct('base/images/bullitlicht1.gif',
+ 'faq');"
+ onmouseout="navDeAct('base/images/bullitdonker.gif',
+ 'faq');"
+ class="vertnavsub">FAQ</a>
+ </td>
+ </tr>
+
<tr>
<td valign="top" width="20">
<img src="base/images/bullitdonker.gif" id="b_exercise">
--
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