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Showing posts with label swissprot database. Show all posts
Showing posts with label swissprot database. Show all posts
Tuesday, November 2, 2010
primary structure analysis:
8:11 AM
GCbioinfo
Tool:
Radar:De novo repeat detection in protein sequences
I entered the protein albumin in uniprot and get the following result It gave the number of repeats present in the sequence.
http://www.ebi.ac.uk/Tools/es/cgi-bin/jobresults.cgi/radar/radar-20101102-1505421645.html
Radar:De novo repeat detection in protein sequences
I entered the protein albumin in uniprot and get the following result It gave the number of repeats present in the sequence.
http://www.ebi.ac.uk/Tools/es/cgi-bin/jobresults.cgi/radar/radar-20101102-1505421645.html
Monday, November 1, 2010
primary structure analysis
7:49 AM
GCbioinfo
Tools:
Radar :De novo repeat detection in protein sequences go to http://www.ebi.ac.uk/Tools/Radar/index.html
Radar :De novo repeat detection in protein sequences go to http://www.ebi.ac.uk/Tools/Radar/index.html
primary structure analysis:
7:39 AM
GCbioinfo
Tools:
HeliQuest A web server to screen sequences with specific alpha-helical properties HeliQuest calculates from an α-helix sequence its physicochemical properties and amino acid composition and uses the results to screen any databank in order to identify protein segments possessing similar features.
The server is divided into 2 interconnected modules: the sequence analysis module and the screening module.
In addition, the mutation module, (available from the sequence analysis module), allows user to mutate helices manually or automatically by genetic algorithm to create analogues with specific properties.-http://heliquest.ipmc.cnrs.fr/
After entering the helix sequence of the protein this protein sequence is get by entering the name of the protein in uniprot then paste it by clicking the analysis button and get the following
http://heliquest.ipmc.cnrs.fr/cgi-bin/ComputParams.py
HeliQuest A web server to screen sequences with specific alpha-helical properties HeliQuest calculates from an α-helix sequence its physicochemical properties and amino acid composition and uses the results to screen any databank in order to identify protein segments possessing similar features.
The server is divided into 2 interconnected modules: the sequence analysis module and the screening module.
In addition, the mutation module, (available from the sequence analysis module), allows user to mutate helices manually or automatically by genetic algorithm to create analogues with specific properties.-http://heliquest.ipmc.cnrs.fr/
http://heliquest.ipmc.cnrs.fr/cgi-bin/ComputParams.py
7:19 AM
GCbioinfo
Tools:
ScanSite pI/Mw:Compute the theoretical pI and Mw, and multiple phosphorylation states. Enter a protein name and sequence below. The molecular weight and isoelectric point of this sequence and multiple phosphorylation states will be displayed. http://scansite.mit.edu/calc_mw_pi.html
out put will be
ScanSite pI/Mw:Compute the theoretical pI and Mw, and multiple phosphorylation states. Enter a protein name and sequence below. The molecular weight and isoelectric point of this sequence and multiple phosphorylation states will be displayed. http://scansite.mit.edu/calc_mw_pi.html
out put will be
primary structure analysis 3:
7:06 AM
GCbioinfo
Tool:
Compute pI/Mw: Compute the theoretical isoelectric point (pI) and molecular weight (Mw) from a UniProt Knowledgebase entry or for a user sequence
now go to this tool and get the required result Please enter one or more UniProtKB/Swiss-Prot protein identifiers (ID) (e.g. ALBU_HUMAN) or UniProt Knowledgebase accession numbers (AC) (e.g. P04406), separated by spaces, tabs or newlines. Alternatively, enter a protein sequence in single letter code. The theoretical pI and Mw (molecular weight) will then be computed. previosly I entered the amino acid sequence and now I am going to enter the uniprot AC#.http://www.expasy.org/cgi-bin/pi_tool
it will give you this format of result so click on the following things according to the instructions mentioned Please select one of the following features by clicking on a pair of endpoints, and the computation will be carried out for the corresponding sequence fragment.
Compute pI/Mw: Compute the theoretical isoelectric point (pI) and molecular weight (Mw) from a UniProt Knowledgebase entry or for a user sequence
now go to this tool and get the required result Please enter one or more UniProtKB/Swiss-Prot protein identifiers (ID) (e.g. ALBU_HUMAN) or UniProt Knowledgebase accession numbers (AC) (e.g. P04406), separated by spaces, tabs or newlines. Alternatively, enter a protein sequence in single letter code. The theoretical pI and Mw (molecular weight) will then be computed. previosly I entered the amino acid sequence and now I am going to enter the uniprot AC#.http://www.expasy.org/cgi-bin/pi_tool
it will give you this format of result so click on the following things according to the instructions mentioned Please select one of the following features by clicking on a pair of endpoints, and the computation will be carried out for the corresponding sequence fragment.
Primary structure analysis 2:
6:51 AM
GCbioinfo
Tool :
ProtParam :Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, isoelectric point, extinction coefficient, etc.)
First go to this page http://www.expasy.org/tools/ select Primary structure analysis and select the first tool as I mentioned. click the tool and I entered the amino acid sequence of protein transgelin-2 in http://www.expasy.org/tools/protparam.html then get the out put page
http://www.expasy.org/cgi-bin/protparam
the out put is
ProtParam :Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, isoelectric point, extinction coefficient, etc.)
First go to this page http://www.expasy.org/tools/ select Primary structure analysis and select the first tool as I mentioned. click the tool and I entered the amino acid sequence of protein transgelin-2 in http://www.expasy.org/tools/protparam.html then get the out put page
http://www.expasy.org/cgi-bin/protparam
the out put is
Primary structure analysis:
6:36 AM
GCbioinfo
Now we are going to the expasy server for the Primary structure analysis of proteins by using different tools available at expasy server.
I will breifly tell you how to use these tools.
I will breifly tell you how to use these tools.
Thursday, August 19, 2010
How to predict the function of unknown or known protein using Swissprot?
4:08 AM
GCbioinfo
First go http://expasy.org/sprot/ search uniprotkb for protein name (opsin 1) then go at this page it will give this protein in many different organism http://www.uniprot.org/uniprot/?query=opsin%201 so narrow down your search click the fields>> and select any option instead of All like organism [OS] so select in next bar human [9606] and click Add&Search the result of protein family present in humans is appeared as a result click any one of the ID so you can get the information about any protein like its domains and function etc http://www.uniprot.org/uniprot/P08100
I hope you will like it regards "Quratt ul ain Siddique"
I hope you will like it regards "Quratt ul ain Siddique"
