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Update: It is working again / Scheduled Downtime 4.-5. May

Update: the downtime is over LiceBase is working.

 

There will be a scheduled Downtime of LiceBase from Monday, 4.5.2015 10.00 am to Tuesday, 5..5.2015 12.00. We are going to do some mandatory maintanance tasks on our database servers. During this time you can experience instability, errors, or down-time of some or all the LiceBase services.

Even if the web-site is available in this period, we advise not to upload data or annotate experiments until we have announced that everything is cleared again.

We appologize for any inconvenience caused.    

 

[UPDATE] No option to extract spliced mRNA or CDS sequence from GBrowse or Tripal

It was noticed that it is not an easy task to extract the spliced mRNA sequence or CDS sequence directly from either GBrowse or Tripal. The annotated sequence of a Gene in Tripal will show the whole gene sequence, as well as the GBrowse CDS track: The CDS track details does not show only the coding sequence but the whole genomic sequence. 

It could be very useful to have an option to easily export only the coding part or only the mature mRNA sequence for designing primers. While it is possible to export a GFF file of the gene model plus the FASTA sequence of the whole chromosome and use an external genome viewer, I assume it might be a good idea to have this feature directly inside GBrowse or Tripal. We are aware of this requirement now and are looking into a solution. I have posted a more detailes question and solution on BioStars https://www.biostars.org/p/135429/

It seems that, until now, there hasn't been a good solution for this in GMOD. Now you can export spliced CDS from GBrowse. Export of the full mRNA, or UTR only, introns only, etc. is not yet implemented, but I am looking into it. 

Repeats track

Repetitive sequences are abundant in most eukaryote genomes. They pose difficulties for an exact reconstruction of the genomic sequence and also for primer design. They can also be useful as genetic markers, as micro- or mini-satelites.

Important: Please annotate phenotype CV

This is an important reminder for the annotation of RNAi experiments.

Please annotate the phenotype correctly after finishing the experiment. To fully annotate the phenotyp, please use the Phenotype CV field on the first page of the annotation, even if you have given a textual annotation of the phenotype. Please use No visible phenotype in case you do not see any phenotype. Please do not write "no phenotype" into the textual phenotype field because there might be an undetected phenotype anyway.

Caligus rogercresseyi transcriptome BLAST database

TSA: Caligus rogercresseyi, transcriptome shotgun assembly

GenBank: GAZX00000000.1

is provided as a BLAST database. If you want to blast against the closest related transcriptome available as of today, visit the BLAST page and select the Caligus rogercresseyi transcriptome database. This is a nucleotide database, most useful probably with a translated BLAST program, either TBLASTN (protein input vs. translated db), or TBLASTX (translated nucleotide query vs translated db).

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