Robert Edgar
Robert Edgar
I'm trying to make a global profile-profile alignment of two MSAs in FASTA format using hhalign (hhsuite-3.3.0-SSE2-Linux), i.e. preserving the columns within each MSA and aligning pairs of columns to...
I believe recombination events can be detected by sliding a window down a genome (or contig) to find the most similar known genomes for each window. Discontinuities in this list...
A good starting point is Pfam_SARS. I reviewed it a few weeks ago, and IIRC it has pretty good coverage of Betacov genes, but doesn't include some of the genes...
We appear to have an unsolved problem with assemblies that have multiple Covs. From @rchikhi in an earlier issue: "Among the 10,816 datasets of the master table, 272 (2.4%) of...
+ Completeness (A1=both UTRs, A2=near-complete, B=most, C=something). ? @rchikhi QC + @taltman UTR annots? + Annotation of genes and other features (@taltman pipeline). + Find closest known full-length genome. **TODO**....
Got this demsg with -b 1 on machine with 64Gb RAM: `Out of memory: Killed process 27429 (diamond) total-vm:69678788kB, anon-rss:64312120kB, file-rss:0kB, shmem-rss:0kB` I'm screening vertebrate chromosomes against a viral proteome...
This is a bug in the current code, I hope to post a fix in the next few days. Work-around is to write a script in python or similar --...
To align a pair of sequences of length L, muscle requires at least 5 x L^2 bytes of memory The upper limit on L is currently a bit less than...
I believe this is fixed in the latest main branch by adding this to the start of `gitver.bash`: if [ ! -d ../.git ] ; then if [ ! -f...