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Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes.

Karpinka JB, Fortriede JD, Burns KA, James-Zorn C, Ponferrada VG, Lee J, Karimi K, Zorn AM, Vize PD - Nucleic Acids Res. (2014)

Bottom Line: All our services have now migrated to a private cloud to achieve better performance and reliability.Researchers can easily navigate from genome content to gene page reports, literature, experimental reagents and many other features using hyperlinks.Xenbase has also greatly expanded image content for figures published in papers describing Xenopus research via PubMedCentral.

View Article: PubMed Central - PubMed

Affiliation: University of Calgary-Computer Science, Calgary, Alberta, Canada.

Show MeSH
The new morpholino support interface. We store data on over 1000 morpholino reagents, gathered from large-scale screens and the Xenopus literature. (A) Each morpholino sequence is aligned to the genome via BLAST and the results for both on-target and potential off-target matches displayed. Various other data, such as publications, utilizing the reagent are also illustrated. (B) Morpholino sequences are also available as a track in our GBrowse implementation. When a user clicks on a morpholino in the browser details on the alignment are displayed in a pop-up window.
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Figure 2: The new morpholino support interface. We store data on over 1000 morpholino reagents, gathered from large-scale screens and the Xenopus literature. (A) Each morpholino sequence is aligned to the genome via BLAST and the results for both on-target and potential off-target matches displayed. Various other data, such as publications, utilizing the reagent are also illustrated. (B) Morpholino sequences are also available as a track in our GBrowse implementation. When a user clicks on a morpholino in the browser details on the alignment are displayed in a pop-up window.

Mentions: The MO interface displays (i) name and synonyms; (ii) mRNA target; (iii) MO type (translation blocking, splice blocking); (iv) sequence; (v) mRNA target alignments and identities; (vi) genomic alignments (including position, identity, mRNA name, on-target/off-target designation and sense/antisense designation) and (vii) attributed publications (Figure 2). The morpholino feature can be accessed at the url, http://www.xenbase.org/reagents/morpholino.do and under the ‘Reagents & Protocols’ drop down menu.


Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes.

Karpinka JB, Fortriede JD, Burns KA, James-Zorn C, Ponferrada VG, Lee J, Karimi K, Zorn AM, Vize PD - Nucleic Acids Res. (2014)

The new morpholino support interface. We store data on over 1000 morpholino reagents, gathered from large-scale screens and the Xenopus literature. (A) Each morpholino sequence is aligned to the genome via BLAST and the results for both on-target and potential off-target matches displayed. Various other data, such as publications, utilizing the reagent are also illustrated. (B) Morpholino sequences are also available as a track in our GBrowse implementation. When a user clicks on a morpholino in the browser details on the alignment are displayed in a pop-up window.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384024&req=5

Figure 2: The new morpholino support interface. We store data on over 1000 morpholino reagents, gathered from large-scale screens and the Xenopus literature. (A) Each morpholino sequence is aligned to the genome via BLAST and the results for both on-target and potential off-target matches displayed. Various other data, such as publications, utilizing the reagent are also illustrated. (B) Morpholino sequences are also available as a track in our GBrowse implementation. When a user clicks on a morpholino in the browser details on the alignment are displayed in a pop-up window.
Mentions: The MO interface displays (i) name and synonyms; (ii) mRNA target; (iii) MO type (translation blocking, splice blocking); (iv) sequence; (v) mRNA target alignments and identities; (vi) genomic alignments (including position, identity, mRNA name, on-target/off-target designation and sense/antisense designation) and (vii) attributed publications (Figure 2). The morpholino feature can be accessed at the url, http://www.xenbase.org/reagents/morpholino.do and under the ‘Reagents & Protocols’ drop down menu.

Bottom Line: All our services have now migrated to a private cloud to achieve better performance and reliability.Researchers can easily navigate from genome content to gene page reports, literature, experimental reagents and many other features using hyperlinks.Xenbase has also greatly expanded image content for figures published in papers describing Xenopus research via PubMedCentral.

View Article: PubMed Central - PubMed

Affiliation: University of Calgary-Computer Science, Calgary, Alberta, Canada.

Show MeSH