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[gofriends] a question

Jack Min jack at gene.concordia.ca
Thu May 17 09:03:26 PDT 2007


Hi Elham,

You may like to try this website - though the output is not exactly you want.

https://fungalgenome.concordia.ca/tools/TargetIdentifier.html

It only support blastx.  However, if you have pre-run blastp, you can also
use this tool to extract the information your want.

Jack


>
> 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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