[Bioclusters] Re: Bioclusters digest, Vol 1 #552 - 3 msgs
Zeng Jin Zhang
bioclusters@bioinformatics.org
Thu, 2 Sep 2004 09:55:04 +0800
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How much is your large genome size(MB/GB)? The assembling method is als=
o
decided by your genome size/repeats complexity. Using parallel phrap ju=
st
can solve simple and small genome assembling.
Email: zengjinz@cn.ibm.com
Notes: Zeng Jin Zhang/China/Contr/IBM@IBMCN
=
bioclusters-reque =
st@bioinformatics =
.org =
To
Sent by: bioclusters@bioinformatics.org =
bioclusters-admin =
cc
@bioinformatics.o =
rg Subj=
ect
Bioclusters digest, Vol 1 #552 -=
3
msgs =
2004-09-02 00:01 =
=
=
Please respond to =
bioclusters =
=
=
Digest etiquette: When replying, PLEASE edit your Subject line so it
is more specific than "Re: Bioclusters digest, Vol..." And, PLEASE
quote only related text -- do not quote the entire digest. Thank you.
Today's Topics:
1. Parallel assembling of a shotgun genome
(=3D?iso-8859-1?Q?Octavio_Mart=3DEDnez_de_la_Vega?=3D)
2. Re: Parallel assembling of a shotgun genome (Joe Landman)
3. Re: Parallel assembling of a shotgun genome (Charles Wust)
--__--__--
Message: 1
From: =3D?iso-8859-1?Q?Octavio_Mart=3DEDnez_de_la_Vega?=3D
<omartine@ira.cinvestav.mx>
To: <bioclusters@bioinformatics.org>
Date: Tue, 31 Aug 2004 12:05:33 -0500
Subject: [Bioclusters] Parallel assembling of a shotgun genome
Reply-To: bioclusters@bioinformatics.org
Hi,
We are a genomic research center in M=3DE9xico and we will be initiatin=
g =3D
the
shotgun sequence of a large genome. Currently we do our bioinformatics
in a 32 processor cluster, but we assemble (for example ESTs sequences)=
using Phrap and/or CAP3.
The question is,
Can I parallelize the assembling of a shotgun sequencing project to use=
the power of a cluster?
Thanks in advance,
Octavio.
------------------------------------
Octavio Mart=3DEDnez de la Vega
Profesor Titular
omartine@ira.cinvestav.mx
Km. 9.6 Lib. Nte., Carretera Irapuato-Le=3DF3n, Apartado Postal 629, CP=
36500 Irapuato, Gto. M=3DE9xico.
tel: (55) 462 6239649
fax: (55) 462 6239660
mobile: 044 462 4822309
------------------------------------
--__--__--
Message: 2
Date: Tue, 31 Aug 2004 13:12:09 -0400
From: Joe Landman <landman@scalableinformatics.com>
To: bioclusters@bioinformatics.org, omartine@ira.cinvestav.mx
Subject: Re: [Bioclusters] Parallel assembling of a shotgun genome
Reply-To: bioclusters@bioinformatics.org
Hi Octavio:
Have a look at SPS Phrap Suite at
http://www.geospiza.com/tools/sps-phrap.htm .
Joe
Octavio Mart=1B$B4Z=1B(Bez de la Vega wrote:
>Hi,
>
>We are a genomic research center in M=1B$B9^=1B(Bico and we will be in=
itiating the
>shotgun sequence of a large genome. Currently we do our bioinformatics=
>in a 32 processor cluster, but we assemble (for example ESTs sequences=
)
>using Phrap and/or CAP3.
>The question is,
>Can I parallelize the assembling of a shotgun sequencing project to us=
e
>the power of a cluster?
>
>Thanks in advance,
>
>Octavio.
>
>------------------------------------
>Octavio Mart=1B$B4Z=1B(Bez de la Vega
>Profesor Titular
>omartine@ira.cinvestav.mx
>
>
--
Joseph Landman, Ph.D
Scalable Informatics LLC,
email: landman@scalableinformatics.com
web : http://www.scalableinformatics.com
phone: +1 734 612 4615
--__--__--
Message: 3
From: Charles Wust <charles@lisha.ufsc.br>
Date: Tue, 31 Aug 2004 18:16:43 -0300 (BRT)
Subject: Re: [Bioclusters] Parallel assembling of a shotgun genome
To: bioclusters@bioinformatics.org
Cc: bioclusters@bioinformatics.org, omartine@ira.cinvestav.mx
Reply-To: bioclusters@bioinformatics.org
Hello,
I am presently doing research in this field, but I do not have any work=
ing
version of a parallel fragment assembler yet.
But look for PCAP. It is made by the same author of CAP3, it should wor=
k
well on your cluster.
Charles
> Hi Octavio:
>
> Have a look at SPS Phrap Suite at
> http://www.geospiza.com/tools/sps-phrap.htm .
>
> Joe
>
> Octavio Mart=1B$B4Z=1B(Bez de la Vega wrote:
>
>>Hi,
>>
>>We are a genomic research center in M=1B$B9^=1B(Bico and we will be i=
nitiating the
>>shotgun sequence of a large genome. Currently we do our bioinformatic=
s
>>in a 32 processor cluster, but we assemble (for example ESTs sequence=
s)
>>using Phrap and/or CAP3.
>>The question is,
>>Can I parallelize the assembling of a shotgun sequencing project to u=
se
>>the power of a cluster?
>>
>>Thanks in advance,
>>
>>Octavio.
>>
>>------------------------------------
>>Octavio Mart=1B$B4Z=1B(Bez de la Vega
>>Profesor Titular
>>omartine@ira.cinvestav.mx
>>
>>
>
>
> --
> Joseph Landman, Ph.D
> Scalable Informatics LLC,
> email: landman@scalableinformatics.com
> web : http://www.scalableinformatics.com
> phone: +1 734 612 4615
>
> _______________________________________________
> Bioclusters maillist - Bioclusters@bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
>
--__--__--
_______________________________________________
Bioclusters maillist - Bioclusters@bioinformatics.org
https://bioinformatics.org/mailman/listinfo/bioclusters
End of Bioclusters Digest
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<html><body>
<p>How much is your large genome size(MB/GB)? The assembling method is =
also decided by your genome size/repeats complexity. Using parallel phr=
ap just can solve simple and small genome assembling.<br>
<br>
Email: zengjinz@cn.ibm.com <br>
Notes: Zeng Jin Zhang/China/Contr/IBM@IBMCN<br>
<img src=3D"cid:10__=3DC7BBE590DF9A7F3B8f9e8a93df938@cn.ibm.com" width=3D=
"16" height=3D"16" alt=3D"Inactive hide details for bioclusters-request=
@bioinformatics.org">bioclusters-request@bioinformatics.org<br>
<br>
<br>
<table width=3D"100%" border=3D"0" cellspacing=3D"0" cellpadding=3D"0">=
<tr valign=3D"top"><td style=3D"background-image:url(cid:20__=3DC7BBE59=
0DF9A7F3B8f9e8a93df938@cn.ibm.com); background-repeat: no-repeat; " wid=
th=3D"40%">
<ul>
<ul>
<ul>
<ul><b><font size=3D"2">bioclusters-request@bioinformatics.org</font></=
b><font size=3D"2"> </font><br>
<font size=3D"2">Sent by: bioclusters-admin@bioinformatics.org</font>
<p><font size=3D"2">2004-09-02 00:01</font>
<table border=3D"1">
<tr valign=3D"top"><td width=3D"168" bgcolor=3D"#FFFFFF"><div align=3D"=
center"><font size=3D"2">Please respond to<br>
bioclusters</font></div></td></tr>
</table>
</ul>
</ul>
</ul>
</ul>
</td><td width=3D"60%">
<table width=3D"100%" border=3D"0" cellspacing=3D"0" cellpadding=3D"0">=
<tr valign=3D"top"><td width=3D"1%" valign=3D"middle"><img src=3D"cid:3=
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100%"><img src=3D"cid:30__=3DC7BBE590DF9A7F3B8f9e8a93df938@cn.ibm.com" =
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<font size=3D"2">bioclusters@bioinformatics.org</font></td></tr>
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100%"><img src=3D"cid:30__=3DC7BBE590DF9A7F3B8f9e8a93df938@cn.ibm.com" =
border=3D"0" height=3D"1" width=3D"1" alt=3D""><br>
</td></tr>
<tr valign=3D"top"><td width=3D"1%" valign=3D"middle"><img src=3D"cid:3=
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<font size=3D"2">Bioclusters digest, Vol 1 #552 - 3 msgs</font></td></t=
r>
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<tr valign=3D"top"><td width=3D"58"><img src=3D"cid:30__=3DC7BBE590DF9A=
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<br>
<tt>Digest etiquette: When replying, PLEASE edit your Subject line so i=
t<br>
is more specific than "Re: Bioclusters digest, Vol..." =
And, PLEASE<br>
quote only related text -- do not quote the entire digest. Thank =
you.<br>
<br>
<br>
Today's Topics:<br>
<br>
1. Parallel assembling of a shotgun genome (=3D?iso-8859-=
1?Q?Octavio_Mart=3DEDnez_de_la_Vega?=3D)<br>
2. Re: Parallel assembling of a shotgun genome (Joe Landm=
an)<br>
3. Re: Parallel assembling of a shotgun genome (Charles W=
ust)<br>
<br>
--__--__--<br>
<br>
Message: 1<br>
From: =3D?iso-8859-1?Q?Octavio_Mart=3DEDnez_de_la_Vega?=3D <omartine=
@ira.cinvestav.mx><br>
To: <bioclusters@bioinformatics.org><br>
Date: Tue, 31 Aug 2004 12:05:33 -0500<br>
Subject: [Bioclusters] Parallel assembling of a shotgun genome<br=
>
Reply-To: bioclusters@bioinformatics.org<br>
<br>
Hi,<br>
<br>
We are a genomic research center in M=3DE9xico and we will be initiatin=
g =3D<br>
the<br>
shotgun sequence of a large genome. Currently we do our bioinformatics<=
br>
in a 32 processor cluster, but we assemble (for example ESTs sequences)=
<br>
using Phrap and/or CAP3.<br>
The question is,<br>
Can I parallelize the assembling of a shotgun sequencing project to use=
<br>
the power of a cluster?<br>
<br>
Thanks in advance,<br>
<br>
Octavio.<br>
<br>
------------------------------------<br>
Octavio Mart=3DEDnez de la Vega<br>
Profesor Titular<br>
omartine@ira.cinvestav.mx<br>
Km. 9.6 Lib. Nte., Carretera Irapuato-Le=3DF3n, Apartado Postal 629, CP=
<br>
36500 Irapuato, Gto. M=3DE9xico.<br>
tel: (55) 462 6239649<br>
fax: (55) 462 6239660<br>
mobile: 044 462 4822309<br>
------------------------------------<br>
<br>
<br>
<br>
--__--__--<br>
<br>
Message: 2<br>
Date: Tue, 31 Aug 2004 13:12:09 -0400<br>
From: Joe Landman <landman@scalableinformatics.com><br>
To: bioclusters@bioinformatics.org, omartine@ira.cinvestav.mx<br>
Subject: Re: [Bioclusters] Parallel assembling of a shotgun genom=
e<br>
Reply-To: bioclusters@bioinformatics.org<br>
<br>
Hi Octavio:<br>
<br>
Have a look at SPS Phrap Suite at <br>
</tt><tt><a href=3D"http://www.geospiza.com/tools/sps-phrap.htm">http:/=
/www.geospiza.com/tools/sps-phrap.htm</a></tt><tt> .<br>
<br>
Joe<br>
<br>
Octavio Mart韓ez de la Vega wrote:<br>
<br>
>Hi,<br>
><br>
>We are a genomic research center in M閤ico and we will be ini=
tiating the<br>
>shotgun sequence of a large genome. Currently we do our bioinformat=
ics<br>
>in a 32 processor cluster, but we assemble (for example ESTs sequen=
ces)<br>
>using Phrap and/or CAP3.<br>
>The question is,<br>
>Can I parallelize the assembling of a shotgun sequencing project to=
use<br>
>the power of a cluster?<br>
><br>
>Thanks in advance,<br>
><br>
>Octavio.<br>
><br>
>------------------------------------<br>
>Octavio Mart韓ez de la Vega<br>
>Profesor Titular<br>
>omartine@ira.cinvestav.mx<br>
> <br>
><br>
<br>
<br>
-- <br>
Joseph Landman, Ph.D<br>
Scalable Informatics LLC,<br>
email: landman@scalableinformatics.com<br>
web : </tt><tt><a href=3D"http://www.scalableinformatics.com">htt=
p://www.scalableinformatics.com</a></tt><tt><br>
phone: +1 734 612 4615<br>
<br>
<br>
--__--__--<br>
<br>
Message: 3<br>
From: Charles Wust <charles@lisha.ufsc.br><br>
Date: Tue, 31 Aug 2004 18:16:43 -0300 (BRT)<br>
Subject: Re: [Bioclusters] Parallel assembling of a shotgun genom=
e<br>
To: bioclusters@bioinformatics.org<br>
Cc: bioclusters@bioinformatics.org, omartine@ira.cinvestav.mx<br>
Reply-To: bioclusters@bioinformatics.org<br>
<br>
Hello,<br>
<br>
I am presently doing research in this field, but I do not have any work=
ing<br>
version of a parallel fragment assembler yet.<br>
<br>
But look for PCAP. It is made by the same author of CAP3, it should wor=
k<br>
well on your cluster.<br>
<br>
Charles<br>
<br>
> Hi Octavio:<br>
><br>
> Have a look at SPS Phrap Suite at<br>
> </tt><tt><a href=3D"http://www.geospiza.com/tools/sps-phrap.htm">h=
ttp://www.geospiza.com/tools/sps-phrap.htm</a></tt><tt> .<br>
><br>
> Joe<br>
><br>
> Octavio Mart韓ez de la Vega wrote:<br>
><br>
>>Hi,<br>
>><br>
>>We are a genomic research center in M閤ico and we will be=
initiating the<br>
>>shotgun sequence of a large genome. Currently we do our bioinfo=
rmatics<br>
>>in a 32 processor cluster, but we assemble (for example ESTs se=
quences)<br>
>>using Phrap and/or CAP3.<br>
>>The question is,<br>
>>Can I parallelize the assembling of a shotgun sequencing projec=
t to use<br>
>>the power of a cluster?<br>
>><br>
>>Thanks in advance,<br>
>><br>
>>Octavio.<br>
>><br>
>>------------------------------------<br>
>>Octavio Mart韓ez de la Vega<br>
>>Profesor Titular<br>
>>omartine@ira.cinvestav.mx<br>
>><br>
>><br>
><br>
><br>
> --<br>
> Joseph Landman, Ph.D<br>
> Scalable Informatics LLC,<br>
> email: landman@scalableinformatics.com<br>
> web : </tt><tt><a href=3D"http://www.scalableinformatics.com=
">http://www.scalableinformatics.com</a></tt><tt><br>
> phone: +1 734 612 4615<br>
><br>
> _______________________________________________<br>
> Bioclusters maillist - Bioclusters@bioinformatics.org<=
br>
> </tt><tt><a href=3D"https://bioinformatics.org/mailman/listinfo/bi=
oclusters">https://bioinformatics.org/mailman/listinfo/bioclusters</a><=
/tt><tt><br>
><br>
<br>
<br>
<br>
--__--__--<br>
<br>
_______________________________________________<br>
Bioclusters maillist - Bioclusters@bioinformatics.org<br>
</tt><tt><a href=3D"https://bioinformatics.org/mailman/listinfo/bioclus=
ters">https://bioinformatics.org/mailman/listinfo/bioclusters</a></tt><=
tt><br>
<br>
<br>
End of Bioclusters Digest<br>
</tt><br>
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