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Hello, I am a novice in biology. Can I use ProTrek for protein sequence alignment?
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PFASUM are matrices built from Pfam structural alignments ([reference](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1703-z)).
The main website is down, but I found their im…
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Hi Brian.
I've moved on to EVM after talking with you about TransDecoder yesterday. I'm trying to use Exonerate protein2genome alignments from a Maker run as input to EVM. I'm am wondering about ge…
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Homology search started at 2024-08-21 08:40:06.163220.
Settings:
Search method: diamond.
Self-alignment method: native.
Remote fetch enabled: no.
Reading input proteins...
Sulfurospirill…
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## Expected Behavior
When i run the easy-cluster wih a set of rfdiffusion generated structures, i obeserve that with foldseek cluster program which based e-value will give the ooposite trend, compar…
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Hi,
I'm new to foldseek and I wonder if you can you provide guidance on how I can obtain structure alignment of a small fragment of a protein. Basically, the protein has a 8-aa forming a beta-hairpin…
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I created unpaired and paired MSAs using jackhmmer searches and created two separate MSA contexts out of them. However, when you combine protein complex modeling with a ligand, the AllAtomStructureCon…
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### Description of feature
Hi Jason,
This workflow looks great and I hope to try it out soon.
If you haven't already considered it, you might want to take a look at incorporating this tool as an a…
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Hi,
First, apologies if this is not the best place to ask this question. I'm doing gene annotation for a non-model rodent, and I have tried several approaches:
1. BRAKER2: with a large protein dat…
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Use blastx to predict protein function from amino acid sequence by comparing to other known proteins using homology and preserved domains, im pretty sure you can also install it as a module in python …