Martin Hölzer
Martin Hölzer
Hi! Lately, I experienced fragmented gene annotations in terms of two (or more) ORFs that are in close proximity and are annotated with homology to the same gene. In such...
Hi! I just tried to reinstall the databases which fails in the step ``` curl -o aa_seq_euk.fasta.gz ftp://cegg.unige.ch/OrthoDB8/Eukaryotes/FASTA/aa_seq_euk.fasta.gz curl: (28) Failed to connect to cegg.unige.ch port 21: Connection timed out...
This might be another interesting tool to add * https://github.com/KennthShang/PhaMer * http://arxiv.org/abs/2201.04778
I just stumbled over this tool: [PhageTerm publication](https://www.nature.com/articles/s41598-017-07910-5) that sounds interesting. It seems they are using different known phage replication strategies (such as DTR, direct terminal repeats) to describe phage...
see https://www.dfg.de/download/pdf/foerderung/programme/sachbeihilfe/info_vordrucksaenderungen.pdf There seems to be some template from DFG for the attached CV? Could be also added to the template, although it also seems fine to just attach any...
... check if changes are needed based on https://twitter.com/pampel/status/1565292116162408448?t=o6_3jI_d2QCrXezwcjvjlQ&s=19
Next to the HTML output, it would be great to have a visualization also in PDF format. Maybe using clustalx or a LaTeX package (e.g. [TexShade](http://mirrors.ibiblio.org/CTAN/macros/latex/contrib/texshade/texshade.pdf)) to draw the alignment...
Currently, PoSeiDon does not have a user-friendly error control and feedback. This can be implemented using functionalities such as ```java annotated_reads .map{ row -> row[-2]} .collect() .subscribe onNext: { for...
At the moment a script checks for some dangerous symbols in FASTA headers. It would be more convenient to initially rename the FASTA headers and then restore them at the...