Difference between revisions of "User:Smith"
 
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==Resources:==
  
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==Tutorial: Promoter Analysis==
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http://geworkbench.org =
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http://wiki.c2b2.columbia.edu/workbench
  
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http://wiki.c2b2.columbia.edu/workbook/index.php/Genomics_Workbook
  
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==Tutorial: Regulatory Network Reverse Engineering==
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https://sharepoint.c2b2.columbia.edu/c2b2/default.aspx
  
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http://wiki.c2b2.columbia.edu/mantis/
  
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==Tutorial: Integrated Annotation Information ???==
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http://wiki.c2b2.columbia.edu/mantis/view_all_bug_page.php
  
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http://wiki.c2b2.columbia.edu/mantis/login_page.php
  
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==Tutorial: Enrichment Analysis/GO Term component==
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http://wiki.c2b2.columbia.edu/isrce/index.php/MARINa,_IDEA,_CUPID_Grid_Service_Implementation
  
  
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==Tutorial: Sequence Analysis - BLAST==
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http://gforge.nci.nih.gov
  
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Use the file "NM_024426-Wilms.fasta" provided in the tutorial data directory. This is a nucleotide sequence file.  There is a second file which contains the corresponding protein sequence, "NP_077744-Wilms.fasta".
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http://gforge.nci.nih.gov/projects/geworkbench
  
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Provide a little background info about Wilm's tumor. (It was chosen at random).
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http://wiki.c2b2.columbia.edu/informatics/
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same as
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(http://helpdesk.cu-genome.org/informatics/)
  
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Go to Sequence Alignment.
 
  
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Select BLAST.
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ICTVdb
  
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Note that the subsequence displays the length of the longest sequence selected (here there is only one).  It can be used to select out a portion of the sequence to use for the query ( probably wouldn't make much sense if more than one sequence is selected for the query).
 
  
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Select a program.  Since this is a nucelotide query, we want to select a nucleotide query program such as blastn.
 
  
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Provide a one line description of each of the different blast algorithms. We have this info on the AMDeC website.
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http://wiki.c2b2.columbia.edu/ictvdb/
  
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Now that the program has been selected, note that the appropriate databases are displayed (need to verify this for all algorithms).  Here we will try ncbi/nt - the complete non-redundant nucleotide database.
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nonpublic documents:
  
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Go to the advanced options tab. Make sure the matrix "dna.mat" is selected.  Change the Expect value to 0.01.  We will leave checked the box to use PFP filtering for repeated sequence elements (Paracel Filtering Package).
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adcvs.cu-genome.org:/cvs/magnet
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In the Service tab, select Columbia.
 
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Note the text field at bottom which shows that one sequence has been selected.  If you have a fasta file with mulitple sequences, you can select the ones you want in the Markers component and activate this selection, letting you search on a subset.  Or, you can search on all the sequences in a file (all markers checkbox, or also by default if no subselection made?  find out).
 
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You can check the server status by hitting the "Refresh" button.  For the columbia machine, this can give you an idea of how busy it is.
 
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Press the curved arrow submit button.  Observe the progress bar "Blast is running".
 

Latest revision as of 13:11, 6 August 2013

Resources:

http://geworkbench.org = http://wiki.c2b2.columbia.edu/workbench

http://wiki.c2b2.columbia.edu/workbook/index.php/Genomics_Workbook

https://sharepoint.c2b2.columbia.edu/c2b2/default.aspx

http://wiki.c2b2.columbia.edu/mantis/

http://wiki.c2b2.columbia.edu/mantis/view_all_bug_page.php

http://wiki.c2b2.columbia.edu/mantis/login_page.php

http://wiki.c2b2.columbia.edu/isrce/index.php/MARINa,_IDEA,_CUPID_Grid_Service_Implementation


http://gforge.nci.nih.gov

http://gforge.nci.nih.gov/projects/geworkbench

http://wiki.c2b2.columbia.edu/informatics/ same as (http://helpdesk.cu-genome.org/informatics/)


ICTVdb


http://wiki.c2b2.columbia.edu/ictvdb/

nonpublic documents:

adcvs.cu-genome.org:/cvs/magnet

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