gapseq
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jotech
Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
Hello! I tried running gapseq doall with E. coli genome and I get the following error when writing the xml file. Wrote file GCA_000005845.2_ASM584v2_genomic.xml Patching file GCA_000005845.2_ASM584v2_genomic.xml ...Error in (grp_block_start...
> for bug reports and errors please report the output of: ./gapseq test Hi, Thank you for the software, I am finding it very useful. I added reactions in different...
Currently, we use TBLASTN to align the genomic sequence to reference protein sequences. This works, but the performance can be improved (in terms of run time) if ORF are predicted...
For example if you have eukaryotic genomes with eukaryotic gene calls, can you use these instead of giving full genomes? If not, can this be an option in the future?
FYI, I created an issue [#275](https://github.com/ebi-uniprot/uniprot-rest-api/issues/275) with UniProt explaining how the new UniProt website & REST API breaks `uniprot.sh` 's querying of UniRef. This may go unnoticed for users of...
Hello, I am going to simulate a community with 3 bacteria, A,B and C. B takes the products of A and C takes the products of B. When generating the...
Dear Gapseq developer, I am super excited about this software. It does improve CarveMe and ModelSeed draft models a lot and it provides a long list of tentative reactions, which...
Hello, I have been testing several media on a model of _Acetobacterium wodii_ and I have encountered some issues with some metabolites present in the growth medium. I am trying...
Hi again, I tried the new function of prediction of carbon sources and fermentation products, and it is useful for me. I can get two lists of the same kind...
