I just finished running my experiment in KEGG - Kaas, analyzing metabolic pathways for the illumina transcriptome (RNA) sequencing data we have, mapping them to Eukaryotes.
I may like to run the same experiment in Metacyc but it is extremely difficult for me to find my way in pathway tools of Metacyc/Ecocyc !!! Could somebody please help?
What I need, I just to know what pathways got mapped and what didn't. The data are from a new specy that as never been annotated.
I am a curator of the MetaCyc database. I realize charly.blanche.t doesn't need an answer any more, as it's been 9 years, but I figure I will provide an answer in case people run into a similar situation in the future.
From what charly.blanche.t said, I gather this was an organism that hasn't been sequenced/annotated before. That means it was not going to be included in BioCyc at the time. If it was a bacterium, one can send an email to biocyc-support@ai.sri.com and ask to have it added to the website, in which case one would have a new database with all the information needed by the next BioCyc release.
However, it sounds like this was a eukaryotic organism, and BioCyc does not add eukaryotic organisms per user requests. So in order to perform this analysis one would have to download the Pathway Tools software (which is free to academia) and install it on a local computer (see https://pathwaytools.com/). The software can generate a new Pathway/Genome Database (PGDB) from an annotated sequence. The process is pretty straight forward, there are videos that describe it on the BioCyc website (see Tutorial #6: Creating a Pathway/Genome Database at https://biocyc.org/webinar.shtml).
If a user runs into difficulties it's always possible to email biocyc-support@ai.sri.com for help. We answer all queries within a day or two at the most.
The new PGDB will contain all the predicted pathways, with the organism's genes attached to the predicted reactions, and it will be possible to query and analyze it to get the answers. In addition, if you run Pathway Tools on a Mac or a Linux computer, once you create the new database you can run it in a web server mode, and access it via a web browser, using the same interface as at the BioCyc website (unfortunately, the Windows version of Pathway Tools cannot run in web server mode, but almost all functions are available via the desktop-mode of the software).).
You can use BioCyc/EcoCyc..go to the "Cellular Overview" and make sure you select the species on the top right of the page. You will get an option to upload your Gene/Compound ID together with some values (if required). You have to make sure that the IDs used by you are recognized in BioCyc. The file has to be a simple tab delimited .txt file and not a .csv/excel file.
