Full alignments are an alignment that is made of the SEED sequences and all hits aligned to the CM model. Rfam used to provide these for all families but stopped because it became computationally expensive to provide. We should look at providing them again. This is basically what rfreport does (rfbuild.pl -a is the key command), so we have some of the code ready to go for this.
Getting a final version may require asking eric to modify rfbuild.pl to do a better job at handling large families and alignments. For now, we should:
[ ] Try to build some by hand. I suggest some of the miRNA families we have reports for
[ ] Automate the building of the alignments into a nextflow pipeline
[ ] Run the pipeline on everything and see which families it fails on
[ ] Reach out to Eric to improve rfbuild to work on all families.
Full alignments are an alignment that is made of the SEED sequences and all hits aligned to the CM model. Rfam used to provide these for all families but stopped because it became computationally expensive to provide. We should look at providing them again. This is basically what rfreport does (
rfbuild.pl -ais the key command), so we have some of the code ready to go for this.Getting a final version may require asking eric to modify
rfbuild.plto do a better job at handling large families and alignments. For now, we should: