hello everybody

4 views
Skip to first unread message

suneha upadhyay

unread,
Oct 26, 2009, 10:34:01 AM10/26/09
to Predict...@googlegroups.com
hello everybody
 
I am looking for the website providing free domain prediction if only amino acid sequense of the protein is known.
could anybody help me with it...
 
 
 
thanks a lot

Suneha Upadhyay
Ph.D (Biochemistry)
New Delhi

Linlin Yan

unread,
Oct 29, 2009, 8:46:16 AM10/29/09
to suneha upadhyay, Predict...@googlegroups.com
How about SMART? http://smart.embl-heidelberg.de/

Kornelius Zeth

unread,
Nov 2, 2009, 3:20:17 AM11/2/09
to Linlin Yan, suneha upadhyay, Predict...@googlegroups.com

http://toolkit.lmb.uni-muenchen.de/hhpred

is a great site!
----------------------------------------------
Kornelius Zeth
Max Planck Institute for Developmental Biology
Dept. Protein Evolution
Spemannstr. 35
72076 Tuebingen, Germany
korneli...@tuebingen.mpg.de
Tel -49 7071 601 323
Fax -49 7071 601 349

Mikhail Fursov

unread,
Nov 2, 2009, 4:05:16 AM11/2/09
to PredictProtein
Hi!

with this tool you can run prediction algorithms locally:
http://ugene.unipro.ru/plugin_sec_struct_predict.html

ketaki v

unread,
Nov 2, 2009, 4:24:37 AM11/2/09
to Linlin Yan, suneha upadhyay, Predict...@googlegroups.com
use ppipred.......its a online server

Ioannides,Constantin

unread,
Nov 2, 2009, 5:47:58 AM11/2/09
to Kornelius Zeth, Linlin Yan, suneha upadhyay, Predict...@googlegroups.com
I am looking for a site providing free translation of a human RNA sequence without start and end. Even to find matches.
Constantin.MDACC, Houston,Texas.

Erik Bongcam-Rudloff

unread,
Nov 2, 2009, 5:57:46 AM11/2/09
to Ioannides,Constantin, Kornelius Zeth, Linlin Yan, suneha upadhyay, Predict...@googlegroups.com
You want to find all Open reading Frames (ORF)?

Then EMBOSS is the tool:

use:
checktrans       Reports STOP codons and ORF statistics of a protein
getorf           Finds and extracts open reading frames (ORFs)
plotorf          Plot potential open reading frames in a nucleotide sequence
showorf          Display a nucleotide sequence and translation in pretty format
sixpack          Display a DNA sequence with 6-frame translation and ORFs


Erik

Renato Froidevaux

unread,
Nov 2, 2009, 4:30:17 PM11/2/09
to predict...@googlegroups.com
Hi !

I have the sequence of a protein and the identification of the
secondary domains in the structure.
I want to simulate the hydrolyse of this protein with preservation of
the secondary domains. Do you know softwares able to make this work to
identify the best enzymes ?

Best regards !

Renato Froidevaux, Ph D/HDR
ProBioGEM Laboratory
IUT"A"-Polytech'Lille-USTL


Erik Rudloff

unread,
Nov 8, 2009, 4:07:27 AM11/8/09
to shaolibing110, PredictProtein
Reference to the EMBOSS package is:

EMBOSS: The European Molecular Biology Open Software Suite (2000) 
Rice,P. Longden,I. and Bleasby,A. 
Trends in Genetics 16, (6) pp276--277


Regards

Erik




On 8 nov 2009, at 03.20, shaolibing110 wrote:




在2009-11-02，"Erik Bongcam-Rudloff" <erik...@mac.com> 写道：
You want to find all Open reading Frames (ORF)?

Then EMBOSS is the tool:

use:
checktrans       Reports STOP codons and ORF statistics of a protein
getorf           Finds and extracts open reading frames (ORFs)
plotorf          Plot potential open reading frames in a nucleotide sequence
showorf          Display a nucleotide sequence and translation in pretty format
sixpack          Display a DNA sequence with 6-frame translation and ORFs


Erik

On 2 nov 2009, at 11.47, Ioannides,Constantin wrote:

Reply all
Reply to author
Forward
0 new messages