User: natasha.sernova
natasha.sernova • 2.9k
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Posts by natasha.sernova
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... Try the following orthologous database.
https://omabrowser.org/oma/home/
Select there 'general search'.
Who knows, it may help you. ...
written 2 days ago by
natasha.sernova • 2.9k
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... As far as I have understood, you have sequences
of several or even many hypothetical proteins from some pathogen?
To annotate them you need to find their known orthologous proteins.
Forget for some time about their length or amounts.
Try the following orthologous database:
https://omabrowser. ...
written 2 days ago by
natasha.sernova • 2.9k
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... Go to NCBI-site: www.ncbi.nlm.nih.gov
find 'protein' in the left menu, insert your GI-number (only number)
it will give you its identifier.
Your protein new identifier is can be found here
https://www.ncbi.nlm.nih.gov/protein/WP_004218885.1? ...
written 11 days ago by
natasha.sernova • 2.9k
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Comment:
C: Swissprot db annotate
... A survey of best practices for RNA-seq data analysis
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4728800/
DESeq vs edgeR Comparison
http://www.gettinggeneticsdone.com/2012/09/deseq-vs-edger-comparison.html
edgeR: differential expression analysis of digital gene expression data
https://www.bioc ...
written 13 days ago by
natasha.sernova • 2.9k
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... There was NCBI-reform in 2014.
Here I saved an old version.
https://www.biostars.org/p/180676/
Will it be helpful to you? I am not sure.
Look also here:
https://www.biostars.org/p/164960/
But here the information you need is current.
https://www.biostars.org/p/58872/ ...
written 4 weeks ago by
natasha.sernova • 2.9k
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... These posts may be helpful:
https://www.biostars.org/p/71737/
https://www.biostars.org/p/55962/
https://www.biostars.org/p/134892/
https://www.biostars.org/p/98922/#98923
https://www.biostars.org/p/169499/
...
written 4 weeks ago by
natasha.sernova • 2.9k
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... https://www.biostars.org/p/281900/
I am sorry, you don't need it. ...
written 4 weeks ago by
natasha.sernova • 2.9k
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... Hopefully it may help:
https://www.biostars.org/p/157836/
https://support.bioconductor.org/p/66003/
https://genome.ucsc.edu/goldenpath/help/multiRegionHelp.html
https://stackoverflow.com/questions/29253412/finding-intergenic-regions
...
written 4 weeks ago by
natasha.sernova • 2.9k
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Comment:
C: Analyzing .fasta file.
... What I’ve found:
The protein family was very well studied some time ago. Thare is an interesting domain here.
To find it you need to aligh protein sequences with muscle or mafft.
https://www.ebi.ac.uk/Tools/msa/muscle/
As to your tree, see the post below:
https://www.biostars.org/p/281285/
Yo ...
written 5 weeks ago by
natasha.sernova • 2.9k
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... Try to use OMA-program or OrthoDB.
https://omabrowser.org/standalone/
Here (link below) you can just insert your protein sequence and see what happens:
https://omabrowser.org/oma/home/
OR use orthodb:
http://www.orthodb.org/
They are mentioned in the following post:
https://www.biostars.org/p ...
written 5 weeks ago by
natasha.sernova • 2.9k
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