Questions tagged [kegg]
The kegg tag has no usage guidance.
15
questions
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13 views
Predicting ATC codes at level 3 in python
I am trying to implement the algorithm implemented in this paper on Python. Basically it is a multi labeling algorithm to make out of sample prediction at level 1 of Anatomical Therapeutic Chemical (...
0
votes
1answer
29 views
After KEGG and GO analysis, how to make tables+phylogenetic trees
hope everyone is ok. I used Trinity to do a de novo transcriptome assembly, then blastp/blastx and then used Blast2GO software to do KEGG and GO analysis. So i got some txt files with header :
for GO
...
0
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0answers
8 views
How to compute module completion ratio of KEGG modules from KO identifiers? (command line)
I was previously using KEGG-MAPLE to compute module completion ratios for metagenome assembled genomes. However, this tool was web only (very frustrating) and also it has been discontinued.
Now I'm ...
0
votes
1answer
79 views
How to represent pathways as mathematical graphs?
I would like to construct a mathematical graph: $G = (E,V, w(E))$ a graph with vertices, edges with weight on them based on a KEGG pathway.
Is there a way to do that with existing tools? If not I ...
3
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0answers
42 views
How to load output from the kegg API in biopython into a pandas dataframe?
Biopython provides a (bit unintuitive) API to access to the Kyoto Encyclopedia of Genes and Genomes (KEGG). I am trying to make use of it, but the output is quite unhandy as a string. What is the best ...
1
vote
1answer
20 views
How to map selected genes to Metabolic pathway Maps
I have a selected Arabidopsis Genome Initiative (AGI) list for RNA seq and proteomics data, how can I map them to metabolic pathway maps to vilualize(e.g. TCA cycle / FA / Photosynthesis) in KEGG or ...
2
votes
0answers
48 views
Number of reactions per metabolic pathway
What is the quickest way to calculate the number of chemical reactions present in each pathway for a given organism and which online database such as Kegg, MetaCyc,Reactome is more helpful/reliable ...
1
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0answers
93 views
Downloading full search results from BlastKOALA?
I have just started using BlastKOALA KEGG which has been useful in annotating (aminoacid) sequences. This is their website: https://www.kegg.jp/blastkoala/
When you get results, there are links for ...
5
votes
3answers
268 views
KEGG FTP vs KEGG API
I was reading the KEGG plea and I found that it doesn't forbid using the KEGG API. Then, what is in the FTP server license for personal use/academic use that it is not covered by the API?
Or I could ...
2
votes
0answers
83 views
Locate KEGG/Reactome pathways in user defined network
I am working on big networks of genes. I want to locate KEGG/Reactome pathways in my network. I have already tried cytoKegg and ReactomeFI (Plugins of Cytoscape), they only give me a list of Pathways ...
2
votes
1answer
44 views
AND or OR gene - protein logical relation in KEGG
How do I know if it is a AND or OR relationship between genes associated with the same enzyme in KEGG? E.g., for EC:1.6.1.2 (http://www.genome.jp/dbget-bin/www_bget?ec:1.6.1.2) does the bacterium ...
1
vote
2answers
298 views
How to interconvert InChI and InChIKey?
I would like to retrieve IDs from several databases using InChI as an input, e.g.
...
3
votes
1answer
249 views
How to retrieve InChI key for KEGG compound?
I would like to retrieve the InChI representation for a given KEGG compound but I fail to find a direct solution for this (preferably doing it via bioservices).
One could do it via ChEBI like this:
...
0
votes
2answers
100 views
How can I find the relevant pathway map from gene-gene or protein-protein interaction list? [closed]
I have some difficulties to understand/interpret the pathway map and how a gene-gene interaction list or DNA sequencing can map into pathways.
In addition what's the difference between MARK/ERK ...
9
votes
1answer
190 views
How to retrieve logical expressions (KO based) for reactions from KEGG?
The completeness of a module can easily be checked by looking at the Definition entry associated with the module. For example, in module M00010, it is given as:
<...
