User: karthic
karthic • 100
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Posts by karthic
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... Hi Piyush,
you can study PPI using ClusterOne. First submit your proteins to Sting DB and fetch the interaction table. Then submit the interaction table to Cytoscape and run ClusterOne on that.
Sample input is below..
node1 interaction node2 combined_score
DappuP317081 combined_score Dap ...
written 12 weeks ago by
karthic • 100
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C: What is Genome-sequencing?
... I believe the user has copied the text from a manuscript and pasted here and trying to figure out the term "Genome Sequencing" in that text mean!! ...
written 3 months ago by
karthic • 100
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C: target gene selection for miRNA
... Sorry that answer was for miRanda output. For targetscan you can select the ones which have low total context++ scores.
KK ...
written 3 months ago by
karthic • 100
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... Ofcourse several times.
Here is the sample command..
> blastn -query query_sequence.fa -db /blastdb/nr -evalue 0.0001 -outfmt
> "6 qseqid sseqid pident qlen length mismatch gapope evalue bitscore
> qcovs" -out blast_output.txt -perc_identity 100.00 -num_threads 5 ...
written 3 months ago by
karthic • 100
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Comment:
C: target gene selection for miRNA
... Hi,
You can filter the targetscan results by selecting the ones having energy threshold less than -20 Kcal/mol. Also check the percentage coverage of your query and you can filter based upon them too.
KK ...
written 3 months ago by
karthic • 100
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... Hi,
You can add ClusterOne app to the Cytoscape and do the cluster analysis and plot the interaction map
KK ...
written 3 months ago by
karthic • 100
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... It may not use all the threads allocated by you. However it uses multiple threads according to its requirement.
KK ...
written 3 months ago by
karthic • 100
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... Hi,
Why dont you try itol [https://itol.embl.de/], it is easy and you can choose whatever color you want,
KK ...
written 4 months ago by
karthic • 100
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... It sounds like you want to do homology modelling of your sequences.
There is an online tool called Rampage, which will give ramachandran plot for your predicted structure and gives the percentage of amino acids present in outlier regions etc.
Also you have an online tool called Prosa, which will c ...
written 4 months ago by
karthic • 100
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... First you need to study about that enzyme, and know its complete pathway and identify how it can be targeted. Find out its active sites. Then from literature or database such as chembl you can identify possible compounds which can target that enzyme.
And later probable you can go for docking, pharm ...
written 4 months ago by
karthic • 100
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