Questions tagged [kegg]

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Refactoring pandas using an iterator via chunksize

This question was also asked on Stack Overflow Bioinformatics rationale eggNOG files can be very big and sump all available RAM for regular to medium sized desktops. I am looking for advice on using ...
M__'s user avatar
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How to extract sequences of a specific gene from genomes, with genomes' .fna, .gff and results from KofamScan?

I am trying to do alignment among orthologs and paralogs of a gene but I encountered some problems. I have came up with a workflow, but the sequences I extracted are not correct. They are of hugely ...
Lily Li's user avatar
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2 votes
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COG Enrichment, the overrepresentation test between annotated transcriptome and a set of annotated gene, eggnog-mapper annotation results

I am dealing with a transcriptome of a species and list of genes selected for a gene enrichment analysis. In order to see what kind of genes in my selected list are overrepresented compared with the ...
se-tima's user avatar
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1 answer
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eggNOG: DNA-DNA or protein-protein orthologue identification?

I'm trying to work out is how reliable/accurate my eggNOG metagenomic outputs are. Critical for this is how its identifying orthologues. Background eggNOG is ...
M__'s user avatar
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3 answers
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Analysis of 4665 proteins in String database

Background I have a data set of 4665 proteins from Phytophthora cactorum and want to analyze them in the String database as other database does not have Phytophthora cactorum for GO or KEGG analysis. ...
Bikal's user avatar
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1 answer
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KEGG retrieve hierarchy for organism in biopython

I want to obtain a direct graph from KEGG as well as the genes present in a single term. While it is pretty easy to get list of genes/compounds that are part of a specific category, I am kinda stucked ...
D.A.'s user avatar
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2 votes
0 answers
71 views

Naming conventions for kegg nodes with multiple genes

So I'm downloading XML files from Kegg using BioConductor and and I'm running into a problem. If we look at HIF-1 signaling pathway we see the node growth factor (GF) on the left hand side, we can ...
Travasaurus's user avatar
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How to annotate list of proteins with KEGG orthology groups?

I've got a list of proteins, complete with Uniprot IDs (for some of them) and gene names. I'd like to group them into orthology groups based on data from KEGG, but I have no idea how to add a column ...
Empiromancer's user avatar
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30 views

What genes are driving a certain pathway

I've currently run pathway analysis on a set of genes. I'm now trying to figure out how to see which genes are driving each pathway. ...
mmpp's user avatar
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1 vote
1 answer
450 views

How to get KEGG pathway names from a list of 'ko' IDs?

I have a list of ko IDs from which I want to get the pathway names. How can I get that? I have tried this link, but it does not give me any result. What to do? ...
deep771992's user avatar
1 vote
2 answers
86 views

Functional Annotation vs Functional Enrichment--which one should I use for Network Analysis?

I am currently working on a network pharmacology project where I am supposed to find out the possible diseases our drug might have an effect on. I am not a bioinformatics student, so my knowledge in ...
Gee3's user avatar
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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 ...
Jim Hat's user avatar
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1 answer
137 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 ...
0x90's user avatar
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3 votes
1 answer
187 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 ...
Soerendip's user avatar
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1 vote
1 answer
37 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 ...
Dendrobium's user avatar
2 votes
0 answers
63 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 ...
MMphysics's user avatar
1 vote
0 answers
186 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 ...
Scientist's user avatar
  • 111
5 votes
3 answers
482 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 ...
llrs's user avatar
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2 votes
0 answers
94 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 ...
Saad's user avatar
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2 votes
1 answer
47 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 ...
5norre's user avatar
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2 votes
2 answers
893 views

How to interconvert InChI and InChIKey?

I would like to retrieve IDs from several databases using InChI as an input, e.g. ...
Cleb's user avatar
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3 votes
1 answer
512 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: ...
Cleb's user avatar
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0 votes
2 answers
108 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 ...
0x90's user avatar
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9 votes
1 answer
215 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: <...
Cleb's user avatar
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