Yannick Wurm comments

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                                            Yannick Wurm

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only for euks/humans?

+1 Most recently assembled genomes are collections of contigs or scaffolds, not chromosomes.

overview is problematic for long genomic sequences

This is somewhat linked to the #302

routes.rb posts to /#{job.id}; should post to REQUEST_URI/{#job.id}

Hi @sammyjava - sorry we just discussed this. For serving on suburis we use the [reverse proxy setup as in the doc](https://sequenceserver.com/doc/#nginx) - and it does work nicely. Thus we...

routes.rb posts to /#{job.id}; should post to REQUEST_URI/{#job.id}

Hum - we've only used nginx so we may be missing something on the apache side.

Maybe remove '*' if it is at the end of protein sequence

!gsub(/X$/, "")

Disable FASTA and FASTA of all hits

This may want to be an option specified at launchtime in the overall config file or as a command line option

Disable FASTA and FASTA of all hits

to protect data, the server-side `get_sequence` would also want to be changed to return an empty string.

Now that we have a [functioning and documented API](https://github.com/wurmlab/sequenceserver/pull/473) , it should be relatively simple to create a galaxy plugin. This should enable galaxy users to send their FASTA sequences...

Alignment overview improvement.

Regarding overlapping HSPs, a minimal example is: * Set things up and get it running ``` git clone [email protected]:wurmlab/sequenceserver.git cd sequenceserver bundle install bundle exec bin/sequenceserver -d spec/database/v5/ ``` *...

Alignment overview improvement.

If I search with: ``` >NP_059488.2modified cytochrome P450 3A4 isoform 1 [Homo sapiens] - modified SKETESHKALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDAVLPNKAPPTYDTV LQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGMFIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFS KKNKDNIDPYIYTPFGSGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLSLGGLLQPEKPVV LKVESRDGTVSGASDFKLSDJFSDLKJxCLVKJBcLVKFGLKERJtlrekjtrelkjfgklJGdFOIUDGFKLJGFdFLGLFDKGJDFLGKJDFLKGJSDNbLKJROtidfkl MALIPDLAMETWLLLAVSLVLLYLYGTHSHGLFKKLGIPGPTPLPFLGNILSYHKGFCMFDMECHKKYGK VWGFYDGQQPVLAITDPDMIKTVLVKECYSVFTNRRPFGPVGFMKSAISIAEDEEWKRLRSLLSPTFTSG KLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFGAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKL LRFDFLDPFFLSITVFPFLIPILEVLNICVFPREVTNFLRKSVKRMKESRLEDTQKHRVDFLQLMIDSQN ``` against the database `2020-11 Swiss-Prot insecta`,...