User: karthic
karthic • 100
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Posts by karthic
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C: Highly similar bacterial genomes
... Thank you, I will have a look and see if they suit me. ...
written 6 months ago by
karthic • 100
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... Hi,
I am searching for some bacterial strains or isolates having very high genome similarity as a model to test a program. Since my knowledge in bacterial genomics is very limited, I would really appreciate if someone suggests the genomes, if possible a paper who have done similar kind of work.
TI ...
written 6 months ago by
karthic • 100
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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 10 months 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 10 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 10 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 10 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 10 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 10 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 10 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 11 months ago by
karthic • 100
Latest awards to karthic
Popular Question
12 months ago,
created a question with more than 1,000 views.
For Genome size estimation using jellyfish
Appreciated
13 months ago,
created a post with more than 5 votes.
For A: perl script for discarding sequences less than 200 nucleotides before running C
Popular Question
13 months ago,
created a question with more than 1,000 views.
For Any methods available to do QC analysis of Pacbio raw data??
Scholar
13 months ago,
created an answer that has been accepted.
For A: perl script for discarding sequences less than 200 nucleotides before running C
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: perl script for discarding sequences less than 200 nucleotides before running C
Popular Question
13 months ago,
created a question with more than 1,000 views.
For Any methods available to do QC analysis of Pacbio raw data??
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