I am trying to generate MSAs for the human proteome using hhblits, but it is taking quite a long time. Does anyone know if there is a database that has precomputed MSAs available for download?
MSA's against other genomes or within human genome?
If across genomes then take a look at NCBI's Homologene project. Ensembl has Compara.
I was looking for within the human genome, but I will take a look at these. Thanks!
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