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I am using a program Orthofiller, which leverages profile hmms of orthogroups to search assemblies (hmmdb) for missing genes using `nhmmer`. When using decently sized fungal genomes (> 60 Mb) nhmmer f…
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Hi!
Is there an option to annotate the output of this software? First I got gene models from FunGAP. Then with SignalP I found the sequences that got the signal peptide and this output was the input …
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What's the correct/preferred way to initiate an iterative search with jackhmmer starting with a profile? Alternatively, this would be like initiating jackhmmer with the `-A` aligned hits output of a p…
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HI,
So, my phate_sequenceAnnotation_main.out have two sections 1) the called genes with annotated the blast results. (2)Translated protein and their blast output. But, I see that most of the annotate…
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**First a prelude**
nhmmer's analysis pipeline largely follows the flow of phmmer/hmmsearch:
- ungapped viterbi filter
- gapped viterbi filter
- Forward filter + Backward
- "domain" definition …
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Hi,
I try to use emapper to annotate predicted gene in linux. I success to run with the parameter '-m diamond'. However, I always failed with the hmmer mode. The command is 'emapper.py -i test.f…
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Hi,
I'm using phmmer for some analyses and my analyses aborted after many weeks due to a short power outrage. Does hmmer have any restore points to restart the calculation from that point on? I didn'…
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Dear @EddyRivasLab,
I'm trying to use `phmmer` to search a single protein query against a custom protein database using the following command
`phmmer -E 1 --qformat afa --tformat afa --cpu 4 PF3…
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Hi @HajkD,
I keep getting this error in the filtering step just before usearch clustering.
Which file is failing to be parsed at this stage?
```
Input: /disk2/nguinkal/Zander_Project/pipelines/L…
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Dear experts,
I would like to receive your help in running isescan,
I typed:
isescan.py /scratch/lephuong07/isescan/E97.fasta /scratch/lephuong07/isescan/proteome /scratch/lephuong07/isescan/hm…