yinlabniu
commented
1 year ago Thanks for the questions. We used three methods to predict substrates (two for CGC substrate prediction, and one for CAZyme substrate prediction, see our dbCAN3 paper and https://bcb.unl.edu/dbCAN2/help.php).
The first file (blastp.out) is the raw blast tabular output between each protein of a CGC against proteins in PULs (from dbCAN-PUL, again see our paper, approach B). From this file, we made the columns 1-5 in the third file sub.prediction.out (see our paper for how).
The second file (dbsub.out) is the raw output from hmmscan search of each protein against dbCAN-sub HMMdb. It is for CAZyme substrate prediction (approach A, https://bcb.unl.edu/dbCAN2/help.php). From this file and cgc_standard.out, we use a majority rule to predict substrate for CGC (approach C, https://bcb.unl.edu/dbCAN2/help.php). The parsed info is added into the columns 6-7 in the third file sub.prediction.out (see our paper for how).
In summary, the third file sub.prediction.out is the final file for substrate prediction for CGCs, combining results from approaches B and C. The other two files are intermediate files that can be checked if you want to know the detailed data on where the substrates are predicted from.
Yanbin
MonaLiu421
Dear linnabrown,
Thank you for developing such a good software. I have encountered some result files that were generated during the use process. However, I am uncertain about the exact meaning and significance of these files. I believe that understanding their purpose would greatly benefit my project and contribute to its overall success. Can you explain to me the meaning of the three files respectively? first one:blastp.out
second one:dbsub.out
third one:sub.prediction.out
Warm regards, Mona