Network Diagram Of Protein Domain Architectures

I have a protein domain which can be associated with various other domains. I got a list of these architectures:

A B C
A A A
A D A A A A
A A A B

I am wondering how to make a directed network diagram out of this information.

cytoscape

• 2,468 views • link

updated 12.1 years ago by Biostar

• written 12.3 years ago by Pappu

0 answers

No answers yet.

More posts like this

Mrbayes Produces Incorrect Tree When Run In Mpi Mode
written 12.3 years ago by Pappu

I constructed a phylogenetic trees of a set of 4 distantly related protein families. In FastTree WAG+CAT20, two protein families seem to come from a …
Snps In Protein Domains
written 12.4 years ago by Dataminer

Hi! I have a list of genomic coordinates along with the mutations that have occurred. Something like this: <pre><code>chromosome 13 27470642 C G chromosome 13 …
Dubious Pfam Domain Annotation Of A Protein
written 12.4 years ago by Pappu

I searched a protein sequence for PfamA protein domain signatures by hmmsearch. It turns out that two related domains have significant E-value <1e-10 and they …
Correlation On A List Of Lists
written 12.9 years ago by suganyasivagurunathan •

I have two list of lists A and B, A and B contain 100 data frames each and the dimension of each data frame is …
Row And Column Names In A Matrix
written 13.1 years ago by deschisandy •

I have the matrix in the following form: <pre><code> A-B A-C A-D A-E B-C B-D B-E C-D C-E D-E GENE 1 GENE 2 GENE 3 …
How Can I Efficiently Parse Hmmer Results To Find Listed Domains And Their Architecture?
written 13.2 years ago by James Ashmore •

I am running hmmscan on a fasta file containing a proteome using Pfam-A.hmm. I would like to parse the output from this scan to collect …
How Can I Generate A Venn Diagram In R For A Given Csv File
written 13.3 years ago by Payal •

Hello, AIM is to check common names between A and B or A and multiple variables I have a CSV file which looks like this... …
Making Network Diagram From Pairs Of Gene Names
written 13.3 years ago by Pappu

I want to make a network diagram from a list of gene pairs and their properties: <pre><code>A B X B C Y A D Z …
Drawing Pfam Domain Architecture Of Many Uniprot Ids
written 13.3 years ago by Pappu

I have hundreds of Uniprot IDs. I want to plot their domain architectures in a single file. I am wondering how to do that. Here …
Protein Protein Or Protein Dna/Rna Interaction Prediction
written 14.1 years ago by Pappu

I want to predict which proteins or DNA or RNA might interact with a given protein. However mostly whatever I find is that databases like …