User: karthic
karthic • 100
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Posts by karthic
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... Dear all,
I would like to get some suggestions/recommendations regarding gene prediction for a repeat rich eukaryote genome. We have pacbio isoseq data for some tissues and also illumina based transcriptomes.
Does the availability of isoseq data mandates any new method or I should just follow the ...
written 1 day ago by
karthic • 100
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... Thanks for your reply.
I have used bedtools fasta, I can force strandedness but it outputs only as nucleotide fasta.
Not sure about AGAT, going to install. But from the list of program names, I am unable to find the requisite one. ...
written 11 weeks ago by
karthic • 100
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... Hi everyone,
I know there are lots of program which can translate the nucleotide fasta to protein fasta in all 6 frames or the frame we desire.
But is there any program which can take genome fasta + gff3 table and give protein fasta as output by taking the strand of each sequence also into consider ...
written 11 weeks ago by
karthic • 100
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... Dear all,
I have alignment two large genomes using `last`. It has given me a maf output file.
Is there any way to get quick summary of the alignment, say how much of genome1 is alignment to genome2??
Thanks,
Karthic ...
written 7 months ago by
karthic • 100
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... Hi Everyone,
I am trying to perform alignment between two large genomes of around 1.5G using `last` by following steps from [here][1]. I face the problem when I run the `maf-swap` program on the maf file.
maf-swap: error: list index out of range
Any suggestions??
Thanks,
KK
[1]: https://g ...
written 8 months ago by
karthic • 100
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... I have the following mummer command, when run in terminal it redirects both output and error (log) to separate files.
mummer -mum Reference.fasta Query.fasta > output.txt 2> err.txt
However the same command when called inside a php as below, it only prints output but not error (log).
...
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Comment:
C: Highly similar bacterial genomes
... Thank you, I will have a look and see if they suit me. ...
written 17 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 17 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 21 months ago by
karthic • 100
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Comment:
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 21 months ago by
karthic • 100
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