groupschoof
commented
9 years ago Dear Biojon,
thank you very much for your feedback.
As you can now read in the updated AHRD manual, we do not recommend the usage of GO and InterPro annotations any more. This further information about protein functions was used due to former requests within genome projects. In fact according to our recent - and soon to be published - findings, AHRD performs excellently without this further input data.
As to the pairwise Blast+ output. We are looking into that. Currently there is only the legacy Blast parser. Please use legacy Blast.
Hi,
There are a few issues with input file format:
1) AHRD does not appear to work with the pairwise blastp output produced using BLAST+ (2.2.29+) 2) It appears that the .tsv output from InterProScan5 does not work as an input 3) Blast2GO (perhaps the software most commonly used to find GO terms) does not seem to be able to produce a .csv output, which software did you use to find GO terms if not Blast2GO?
I notice AHRD was used as one of tools for the functional annotation of the wheat genome (http://www.sciencemag.org/content/345/6194/1251788.abstract) (noted in supplemental information). I cannot imagine they used the old version of any of these programs to produce input for AHRD, so I wonder, is there a workaround or alternative solution for these issues?