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[gofriends] a question

Dieter Maier dieter.maier at biomax.com
Wed May 16 02:14:31 PDT 2007


MIPS (Munich information center for protein science) provides SIMAP (similarity matrix of proteins) which is an
all-against-all matrix of all public protein sequences.

http://mips.gsf.de/simap/

Dieter

Barry Zeeberg wrote:

> NCBI probably does an all against all BLAST like you need. Maybe contact the
> help desk at NCBI to see if they have the output files available for
> download.
> 
> Barry
> 
> 
> On 5/9/07 1:56 PM, "Elham Khabiri" <elhamrose at yahoo.com> wrote:
> 
> > Hello every one.
> >   
> >  
> >   
> > I plan to work with a measure to calculate the semantic similarity between
> > genes or proteins and evaluate them with the sequence similarity measure like
> > E-value and Bit Score taken from Blast tool of those gene/protein pairs.
> >   
> >  
> >   
> > Does any body have a set ready like the following so that I can work with
> > those genes and proteins to apply my measure on them? It is so difficult for
> > me to get the bit score and e-value for 1000-2000 gene/protein pairs using the
> > blast tool available online. The set that I need has the following format:
> >   
> >  
> >   
> > Gene1      Gene2        E-value   Bit score
> >   
> > or 
> >   
> > Protein1   Protein 2    E-value   Bit score
> >   
> >  
> >   
> >  
> >   
> > I do appreciate it in advance.
> >   
> >  
> >   
> > Elham
> >   
> > 
> > Ahhh...imagining that irresistible "new car" smell?
> >  Check out new cars at Yahoo! Autos.
> > <http://us.rd.yahoo.com/evt=48245/*http://autos.yahoo.com/new_cars.html;_ylc=X
> > 3oDMTE1YW1jcXJ2BF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDbmV3LWNhcnM->
> 
> 
> <HTML>
> <HEAD>
> <TITLE>Re: [gofriends] a question</TITLE>
> </HEAD>
> <BODY>
> <FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>NCBI probably does an all against all BLAST like you need. Maybe contact the help desk at NCBI to see if they have the output files available for download.<BR>
> <BR>
> Barry<BR>
> <BR>
> <BR>
> On 5/9/07 1:56 PM, "Elham Khabiri" <elhamrose at yahoo.com> wrote:<BR>
> <BR>
> </SPAN></FONT><BLOCKQUOTE><FONT SIZE="4"><FONT FACE="Times New Roman"><SPAN STYLE='font-size:14.0px'>Hello every one.<BR>
> </SPAN></FONT></FONT><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>  <BR>
> </SPAN></FONT><FONT SIZE="4"><FONT FACE="Times New Roman"><SPAN STYLE='font-size:14.0px'> <BR>
> </SPAN></FONT></FONT><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>  <BR>
> </SPAN></FONT><FONT SIZE="4"><FONT FACE="Times New Roman"><SPAN STYLE='font-size:14.0px'>I plan to work with a measure to calculate the semantic similarity between genes or proteins and evaluate them with the sequence similarity measure like E-value and Bit Score taken from Blast tool of those gene/protein pairs. <BR>
> </SPAN></FONT></FONT><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>  <BR>
> </SPAN></FONT><FONT SIZE="4"><FONT FACE="Times New Roman"><SPAN STYLE='font-size:14.0px'> <BR>
> </SPAN></FONT></FONT><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>  <BR>
> </SPAN></FONT><FONT SIZE="4"><FONT FACE="Times New Roman"><SPAN STYLE='font-size:14.0px'>Does any body have a set ready like the following so that I can work with those genes and proteins to apply my measure on them? It is so difficult for me to get the bit score and e-value for 1000-2000 gene/protein pairs using the blast tool available online. The set that I need has the following format:<BR>
> </SPAN></FONT></FONT><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>  <BR>
> </SPAN></FONT><FONT SIZE="4"><FONT FACE="Times New Roman"><SPAN STYLE='font-size:14.0px'> <BR>
> </SPAN></FONT></FONT><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>  <BR>
> </SPAN></FONT><FONT SIZE="4"><FONT FACE="Times New Roman"><SPAN STYLE='font-size:14.0px'>Gene1      </SPAN></FONT></FONT><FONT FACE="Times New Roman"><SPAN STYLE='font-size:12.0px'>Gene2        E-value   Bit score<BR>
> </SPAN></FONT><SPAN STYLE='font-size:12.0px'><FONT FACE="Verdana, Helvetica, Arial">  <BR>
> </FONT></SPAN><FONT SIZE="4"><FONT FACE="Times New Roman"><SPAN STYLE='font-size:14.0px'>or <BR>
> </SPAN></FONT></FONT><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>  <BR>
> </SPAN></FONT><FONT SIZE="4"><FONT FACE="Times New Roman"><SPAN STYLE='font-size:14.0px'>Protein1   </SPAN></FONT></FONT><FONT FACE="Times New Roman"><SPAN STYLE='font-size:12.0px'>Protein 2    E-value   Bit score<BR>
> </SPAN></FONT><SPAN STYLE='font-size:12.0px'><FONT FACE="Verdana, Helvetica, Arial">  <BR>
> </FONT></SPAN><FONT SIZE="4"><FONT FACE="Times New Roman"><SPAN STYLE='font-size:14.0px'> <BR>
> </SPAN></FONT></FONT><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>  <BR>
> </SPAN></FONT><FONT SIZE="4"><FONT FACE="Times New Roman"><SPAN STYLE='font-size:14.0px'> <BR>
> </SPAN></FONT></FONT><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>  <BR>
> </SPAN></FONT><FONT SIZE="4"><FONT FACE="Times New Roman"><SPAN STYLE='font-size:14.0px'>I do appreciate it in advance.<BR>
> </SPAN></FONT></FONT><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>  <BR>
> </SPAN></FONT><FONT SIZE="4"><FONT FACE="Times New Roman"><SPAN STYLE='font-size:14.0px'> <BR>
> </SPAN></FONT></FONT><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>  <BR>
> </SPAN></FONT><FONT SIZE="4"><FONT FACE="Times New Roman"><SPAN STYLE='font-size:14.0px'>Elham<BR>
> </SPAN></FONT></FONT><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>  <BR>
> <HR ALIGN=CENTER SIZE="1" WIDTH="100%">Ahhh...imagining that irresistible "new car" smell?<BR>
>  Check out new cars at Yahoo! Autos. <a href="http://us.rd.yahoo.com/evt=48245/*http://autos.yahoo.com/new_cars.html;_ylc=X3oDMTE1YW1jcXJ2BF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDbmV3LWNhcnM-"><http://us.rd.yahoo.com/evt=48245/*http://autos.yahoo.com/new_cars.html;_ylc=X3oDMTE1YW1jcXJ2BF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDbmV3LWNhcnM-></a> <BR>
> </SPAN></FONT></BLOCKQUOTE><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'><BR>
> </SPAN></FONT>
> </BODY>
> </HTML>
> 

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