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4 votes

How to interconvert InChI and InChIKey?

Recently I've developed a python lib for converting InChI to InChIKey: https://github.com/liwt31/chembl_ikey. Maybe it will help.
liwt31's user avatar
  • 141
2 votes
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How to retrieve InChI key for KEGG compound?

I'm not aware of a functionality in the KEGG service that would allow you to do that directly. I believe your solution (using e.g. ChEBI) is the correct one. You may have other useful service such ...
user1678's user avatar
2 votes

How can I find the relevant pathway map from gene-gene or protein-protein interaction list?

As you alluded to in your question, KEGG does provide a curated set of enzyme and metabolite information. This information can be parsed and used to create a network that you can analyze to look at ...
G_Hannigan's user avatar
2 votes

How can I find the relevant pathway map from gene-gene or protein-protein interaction list?

See a project like Plant reactome, where they infer the pathways of all sequenced plant genomes using orthology to well annotated species. http://plantreactome.gramene.org/
Dan's user avatar
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2 votes
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KEGG FTP vs KEGG API

I found the way to download the genes and pathways thanks to this answer using KEGGREST. It seems that the API allows to fully download the database because it allows to download info, list, find, ...
llrs's user avatar
  • 4,713
2 votes

KEGG retrieve hierarchy for organism in biopython

Ok realized it was much easier than expected. On KEGG it is possible to DL a json file, which is intrinsically ordered. So this parses it into a df ...
D.A.'s user avatar
  • 31
2 votes
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How to get KEGG pathway names from a list of 'ko' IDs?

You can use the KEGG API: ...
zorbax's user avatar
  • 769
1 vote

MEGA11 gives the error "stop codons are found in the translated sequences", even though there are not!

The solution is very simply, MegaX will not allow any stop codons within the "translated" sequence. The reason is simple MEGAX's function is phylogenetic models with nucleotide or protein ...
M__'s user avatar
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1 vote

How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?

Consider filtering on every parameter: Gene Significance (GS), p-value for Gene Significance (p.GS), Module Membership (MM), and p-value for Module Membership (p.MM). This doesn't mean you need to ...
BigMistake's user avatar
1 vote
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How to extract sequences of a specific gene from genomes, with genomes' .fna, .gff and results from KofamScan?

The answer is very simple, just align from amino acids. Amino acids are not subject to saturation - which is what you are encountering and is smashing up the nucleotide alignment. Amino acid will ...
M__'s user avatar
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1 vote
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eggNOG: DNA-DNA or protein-protein orthologue identification?

I can answer this now. I've been 'under the hood' of eggNOG and its using "hmm" (hidden Markov model) very likely, almost certain, the Eddie (sp?) group's ...
M__'s user avatar
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1 vote

Analysis of 4665 proteins in String database

I didn't even know STRING has the kind of analysis you are requesting, I don't see it on their webpage. In any case, the standard tool for GO or KEGG analyses, at least back when I was doing this sort ...
terdon's user avatar
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1 vote

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

The answer to your main doubt about "annotation vs. enrichment" is that you need both, but you already have one annotation. You can only perform a functional enrichment analysis after you ...
Lucio Queiroz's user avatar
1 vote

After KEGG and GO analysis, how to make tables+phylogenetic trees

I'm going to answer 1+2 because 3 is hard to understand and maybe trivial? Each of 1+2 seems to be have these sub-tasks: identify the contigs in your assembly that have the genes of interest. pull ...
Maximilian Press's user avatar
1 vote

How to represent pathways as mathematical graphs?

Pathways are generally directed graphs, which can be implemented in python using the networkx package. Note that there will be cycles in graphs. Please note that ...
Devon Ryan's user avatar
  • 19.6k
1 vote

How to load output from the kegg API in biopython into a pandas dataframe?

solution from @sören: I came up with this solution for my problem: ...
1 vote
Accepted

How to map selected genes to Metabolic pathway Maps

KEGG has a webtool for this, KEGG Mapper. You can just copy-paste your gene ids in there and see how your pathways are colored.
benn's user avatar
  • 3,571
1 vote

KEGG FTP vs KEGG API

If you like to get pathways and corresponding genes as simple table format in a plain text file, use GeneSCF 'prepare_database' module. This can be simple solution. FTP vs API: The differences I see ...
EagleEye's user avatar
1 vote

AND or OR gene - protein logical relation in KEGG

The enzyme EC:1.6.1.2 is an NAD(P) transhydrogenase and consists of two subunits. The two subunits are encoded by two different genes pntA and pntB. So in terms of computer logic I would say AND, ...
benn's user avatar
  • 3,571
1 vote

How to interconvert InChI and InChIKey?

Not sure if directly possible in bioservices but one can do the following workaround using chemspider: ...
Cleb's user avatar
  • 743
1 vote

How to retrieve logical expressions (KO based) for reactions from KEGG?

Some information seems to be available on the module level utilising the API. Reaction R00352 points to the module M00173. While some information is in the ...
ellimilial's user avatar

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