User: Farhad

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Farhad10
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10
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New User
Location:
Turkey
Last seen:
3 years, 3 months ago
Joined:
5 years, 4 months ago
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Posts by Farhad

<prev • 9 results • page 1 of 1 • next >
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Topological features of proteins for Human protein Interactome
... Dear all, I'm looking for a data base to find topological features of human proteins within human interactome. Like degree of each protein or clustering coefficient. Thanks a lot. ...
ppi toplogical features proteins human interactome written 3.3 years ago by Farhad10
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Comment: C: Extracting domain list for proteins Using UniProt.ws in R
... Thanks for your reply, I tried empty string but it doesn't work. I try to write my own query. ...
written 3.5 years ago by Farhad10
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Extracting domain list for proteins Using UniProt.ws in R
... I encountered a problem using uniprot.ws package from R. I want to get interpro domains for list of uniprot IDs using following command: up <- UniProt.ws(taxId=9606) select(up, keys=c("O76064"), columns=c("INTERPRO"),  keytype="UNIPROTKB") if I want to get these information for different or ...
domain R bioconductor uniprot packag written 3.5 years ago by Farhad10 • updated 19 months ago by brennanpincardiff200
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A tool for computing Gene Ontology Semantic Similarity
... I want to compute semantic similarity of proteins given their uniprotID, I have found some online tools like http://www.paccanarolab.org/gosstoweb/, but it is busy all the time and providing organism name is required, I have a mixed list of proteins which include some viral proteins, any similar o ...
gene R sequencing written 4.3 years ago by Farhad10 • updated 4.3 years ago by Jean-Karim Heriche19k
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Finding Domain-Domain interaction score
... I want to find domains of proteins and then calculate a measure using number of their interacting domains. I can use Uniprot to retrieve domains and   'domine' ( http://domine.utdallas.edu/cgi-bin/Domine?page=start) to find interaction between domains manually. Is there any R package, source code ...
R sequence written 4.5 years ago by Farhad10
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Comment: C: Same Protein Sequence
... Thanks again for your comment, about my mentioned examples  http://www.uniprot.org/uniprot/Q68149  and http://www.uniprot.org/uniprot/Q6QY91  both are listed as primary which have same sequence. In this case it seems that I can consider only unique sequences!!! to be sure about duplicate free data ...
written 4.5 years ago by Farhad10
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Comment: C: Same Protein Sequence
... Thanks for detailed reply, If my goal will be creating a data set from known and verified interactions between human and HCV proteins, I Use Data Bases Like http://www.phisto.org/, how should I remove duplicate interactions.  Thanks for your help.   ...
written 4.5 years ago by Farhad10
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Same Protein Sequence
... I'm a beginner in bioinformatics, sorry for asking this question! When I  have two different Uniprot-IDs for two proteins with exactly same sequence, how should I interpret this? are these same protein? Example : Q68149 , Q6QY91 and I know that hepatitis C virus (HCV) has about 11 proteins, but w ...
sequence written 4.5 years ago by Farhad10 • updated 4.5 years ago by pld4.8k
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Bioinformatics And Graph Platforms Like "Powergraph" Or "Graphlab"
... I am new to Bioinformatics, Graph Platforms like "PowerGraph" and "GraphLab" are introduced to process large scale, social and natural graphs, I'm looking for their usage in Bioinformatics, i appreciate your help in advance. ...
bioinformatics parallel graph written 5.3 years ago by Farhad10 • updated 5.3 years ago by Mikael Huss4.6k

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