Do any one have an experience in using plant cyc database? I have done the blastx of my assembled transcriptome with plantcyc.fasta file. The outfmt6 file generated shown some IDs only and no details of corresponding pathways and name of the enzymes. Searching each id for corresponding enzymes and pathway seems tedious due to large number of query. Can any one please suggest whether i have to specify more options or need to upload the IDs to any other tool?
Helo Nadiya,
I have used Plantcyc for rice. I have specifically used it for rice using ricecyc available on Gramene website. You can use a two or more column file containing the ID (the one you retrieved in BLAST) and some value (Expression value) over here. http://pmn.plantcyc.org/overviewsWeb/celOv.shtml
please let me know if you need some more help.
Cheers.
Vinay
Hi vinay,
Thanks for your support. actually i am working on a non model plant. After registration the PMN community send me the link for plantcyc database download. BlastX was performed using linux commands.The URL provided above has some error. I didnt understood, do i have to use the blast results for pathway annotation or i have to make some other corrections.
Hi Nadiya,
I have checked the website. It is temporarily down. So you have to wait for some time.
Now let say you have a transcript A in your assembly for which you want to know the pathway. You blast it with PlantCyc Database which gives you best similarity with B. So the file to be uploaded to the above url should be something like this.
B Some integer
Do this for all your hits.
Hope this clears your doubt.
Cheers..
Vinay
Hello Nadiya,
In the PlantCyc download page there are some files for pathway analysis
for example if you blasted your data against Plantcyc Enzymes v10.0 you should use this one:
ftp://ftp.plantcyc.org/Pathways/Data_dumps/PMN10_June2015/plantcyc_pathways.20150608
Therefore you have 2 files: 1- your tab deliminated blast result file 2- plantcyc-pathway file
By some data mining methods such as grep, awk, or join command in UNIX, using R or other data mining software you can easily join these two files to have one integrated file including your query IDs, gene names, pathway name, EC, and ....
If you need more help, just let me know,
Ahmad
Hi Ahamed,
Thank you so much. Really a great information. I was just individually searching the pathways. Let me try with this option.
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