I'm using blast2go to find GO mappings and annotations by importing protein sequences and their blastp hits, rather than running blastp within blast2go. However, only 7% of the proteins with blastp hits mapped to GO terms. This is very strange because I previously ran a version of this data set before I removed a very small number of genes that were bacterial contamination of the read libraries, and 40% of the proteins with blastp hits mapped to GO terms. I checked the formatting of the xml files from blastp for both data sets, and they appear identical. Has anyone encountered this problem? Is there a fix?
I tried the mapping again and got 36% maps for proteins with blastp hits. I have no idea why there was a difference between runs and to not think it worthwhile trying to figure out why.
I tried the mapping again and got 36% maps for proteins with blastp hits. I have no idea why there was a difference between runs and to not think it worthwhile trying to figure out why.
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