I recently tried to annotate two assembled metagenome samples derived from the same sample type (both samples come from the same type of material) using blastp and the metagene gene predictor tool (via WebMGA). I get a similar number of ORFs predictions for both samples. However after I input these ORF predictions into blastp (same settings for both samples) the number of blastp outputs for one sample were much higher than for the other sample. Why would I get more blastp hits for samples with a similar number of ORFs predicted?
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