general-faq.html
来自「EM算法的改进」· HTML 代码 · 共 121 行
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<!---#### $Id: general-faq.html 1339 2006-09-21 19:46:28Z tbailey $#### $Log$## Revision 1.4 2006/03/07 23:30:20 nadya## merge branches v3_5_1 and v3_5_2 back to the trunk#### Revision 1.3.6.1 2006/02/22 20:49:02 nadya## enabling styling with js and css#### Revision 1.3 2005/09/16 01:17:13 nadya## update main link#### Revision 1.2 2005/08/24 05:28:16 nadya## update links#### Revision 1.1 2005/08/18 05:14:36 nadya## added email checking####---><HTML><HEAD><TITLE>GENERAL - FAQ</TITLE><script src="template-css.js" type="text/javascript"></script></HEAD><body class="body"> <script src="template-header.js" type="text/javascript"></script> <HR> <H3>Frequently Asked Questions</H3> <!-- Developers: When you add a new question, 1) Update next available tag section by adding 1.2) Add the question first to the table of contents. 3) Add the question and answer to the answers section.--> <!--Next available tag: Q002--> <HR> <!-- Table of Contents --> <UL> <LI> <A HREF="#Q001"> <B>Q.</B> I haven't received my MEME results by mail, and it's been more than a day. What happened to my results? <LI> <A HREF="#Q002"> <B>Q.</B> Is there a job queue that I can see how busy the cluster is? <LI> <A HREF="#Q003"> <B>Q.</B> Why don't the motif occurrences in the "Summary of Motifs" block diagrams match the occurrences shown in the individual motif block diagrams? <LI> <A HREF="#Q004"> <B>Q.</B> MAST returns "Your sequence contains unrecognized characters..." <LI> <A HREF="#Q005"> <B>Q.</B> Is it possible to introduce specific amino acid compoistions in the MEME and MAST programs? </UL> <HR> <!-- Answers --> <UL> <A NAME="#Q001"></A> <LI> <B>Q.</B> I haven't received my MEME results by mail, and it's been more than a day. What happened to my results? <P> <B>A.</B> First of all, you should have received a confirmation email that your job is submitted. If you haven't received this email, then you might have typed in the wrong email address. Currently we are requiring users to confirm their email addresses by entering it a second time. <P> While MEME jobs finish typically within 2 hrs when there is no waiting in the queue. It may take up to 1 day if the server gets busy. <br> <br> Alternatively, your mail program may be filtering the MEME results as spam, so check your folders designated as Junk E-mail or Spam. Try to configure your mail program not to filter out emails from <a href="mailto:meme@nbcr.net">meme@nbcr.net</a>. <br> <br> Please also check with your mail server administrator and see whether your email has been filtered out by spam filters ran automatically on all incoming messages by your organization. <br> <br> Finally, you can try using a different email address (hotmail or gmail, etc.). This often solves the problem where you only receive a confirmation message but not the search results. </UL> <HR> <UL> <LI> <A NAME="#Q002"></A> <B>Q.</B> Is there a job queue that I can see how busy the cluster is? <P> <B>A.</B> Yes, we run all MEME jobs on a rocks cluster, and it comes with a built in web interface to the job queue. It can be <a href="http://meme.nbcr.net/ganglia/addons/rocks/queue.php?user=meme&sortby=id&sortorder=up&update=1">accessed here.</a> <P> In your confirmation email, you are given a MEME JOB ID, which is a randomly generated number for each job. <P> You may check the status of your job with the MEME JOB ID by looking at the job info <a href="http://meme.nbcr.net/ganglia/addons/rocks/queue.php?user=meme&sortby=id&sortorder=up&update=1">given here.</a> <P> <P> Currently the MEME JOB ID is indicated only for active jobs running on the clusters, and appears in the job name column as "meme.(MEME_JOB_ID).script". The first column "Id" is the batch job ID for the Sun Grid Engine, a batch scheduler. </UL> <HR> <UL> <A NAME="#Q003"></A> <LI> <B>Q.</B> Why don't the motif occurrences in the "Summary of Motifs" block diagrams match the occurrences shown in the individual motif block diagrams? <P> <B>A.</B> This is a feature, not a bug. The motif occurrences shown for a motif in its section of the output are the ones discovered by the MEME algorithm. These occurrences are then used to create a position specific scoring matrix (PSSM) for the motif. The PSSMs for all of the motifs discovered by MEME are then used to search for non-overlapping sets of occurrences of motifs with p-values under 0.0001 using the MAST algorithm. These are displayed in the "Summary of Motifs" block diagram. Individual motif occurrences will sometimes be missing from the "Summary of Motifs" block diagram because of the non-overlapping or minimum p-value requirements. Conversely, there may be motif occurrences in the summary diagram that were not discovered by the MEME algorithm. </UL> <HR> <UL> <A NAME="#Q004"></A> <LI> <B>Q.</B> MAST returns "Your sequence contains unrecognized characters..." <P> <B>A.</B> The file must be a <B>plain text</B> file. MSWord files, for example, are <B>not</B> acceptable. MSWord files can be converted to plain text by: <BR>"File"-->"Save As"-->"Save As Type"-->"Plain Text' (*.txt). </UL> <HR> <UL> <A NAME="#Q005"></A> <LI> <B>Q.</B> Is it possible to introduce specific amino acid compoistions in the MEME and MAST programs? <P> <B>A.</B> MEME can utilize higher-order background models. This requires a locally installed MEME and running "fasta-get-markov", which is included in the distribution. The switch to MEME is "-bfile". Would be nice to make uploading such a file possible via the web server. <br><br> MAST can use 0-order (composition only) models. This is done automatically on the web server when searching the "upstream" databases using a file based on all upstream regions for the particular organism. As with MEME, users of locally installed MAST can specify their own background files. The switch to MAST is "-bfile". Would be nice to make uploading such a file possible via the web server. </UL> <HR><!--Click here for<A HREF="mast-intro.html"><B>more information</B></A>on <B>MAST</B>.--><BR><font> Return to <A HREF="intro.html"><B>MEME SYSTEM introduction</B></A>. </font> <P> <I>Please send comments and questions to: <A HREF="mailto:meme@nbcr.net">meme@nbcr.net</A>.</B></FORM> </TABLE><script src="template-footer.js" type="text/javascript"></script></body></html>⌨️ 快捷键说明
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