User: DK

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DK80
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Canada
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Posts by DK

<prev • 129 results • page 1 of 13 • next >
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Error wiht MUMMER mapview
... Dear Friends, I am using mummer to align my assembled query phage with the reference genomes (more than 1 obtained from blast hit). In this case the reference genome sequence ins 1 and query sequence is 1. I would really appreciate your suggestions on this error from Mummer: When I run: ./ma ...
mapview genome mummer written 6 days ago by DK80
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Comment: C: Genome alignment with good pictorial representation of genome structure (with an
... Thanks Lieven! I am trying ACT; however, I don't think ACT does genome alignment? It only performs pairwise comparison. Am I right? Any idea on a tool to do a significantly accurate genome alignment? Thanks for your time. ...
written 10 days ago by DK80
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Genome alignment with good pictorial representation of genome structure (with annotated genes)
... Dear Friends, I have been looking for a program or tool for genome alignment (in my case phages). I have an assembled phage and multiple genomes from BLAST hit; I annotated the genes in these phages using DNAMaster, and now, I want to align these genomes against each other and have been looking for ...
gene genome structure gene annotation written 13 days ago by DK80 • updated 13 days ago by h.mon23k
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Comment: C: Best and reliable way to annotate genes? Here the genes belong to a assembled ph
... Thanks! I will work on these ideas and let you know. I think using DNAmaster for the genomes not present in phagesdb website is not a good idea as one needs to polish the sequence for analysis. I am thinking of using Glimmer, GeneMark and then annotating these genes using using BLast and/or use the ...
written 26 days ago by DK80
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Comment: C: Best and reliable way to annotate genes? Here the genes belong to a assembled ph
... Thanks Natasha! I totally agree! But, prediction of genes by softwares like Glimmer, DNAmaster etc might predict some new genes - I think that could be one reason for researchers to use such softwares; do you agree? Moreover, DNAmaster is so widely used for prediction and annotation; however, the so ...
written 27 days ago by DK80
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Comment: C: Best and reliable way to annotate genes? Here the genes belong to a assembled ph
... Thanks Natasha! I already have the phage genome from NCBI; since I am using DNAmaster, it is said in its tutorial that one should use the phage genome from their phagesdb website only as it is a "finished/polished" sequence which is important for gene prediction and annotation. But since I don't fin ...
written 27 days ago by DK80
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Comment: C: Best and reliable way to annotate genes? Here the genes belong to a assembled ph
... Just an edit to my above query: I went to https://phagesdb.org/data/ and to: Full List of GenBank Accession Numbers With phage names Just accession numbers and downloaded the list "With phage names" and looked for the accession of my phage of interest "KP010413" but , could nto f ...
written 27 days ago by DK80
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Comment: C: Best and reliable way to annotate genes? Here the genes belong to a assembled ph
... Hi Natasha, From NCBI I get this page for the phage https://www.ncbi.nlm.nih.gov/nuccore/KP010413.1/ Submission information is as below: ORGANISM Salmonella phage vB_SPuM_SP116 Viruses; dsDNA viruses, no RNA stage; Caudovirales; Myoviridae; Ounavirinae. ...
written 27 days ago by DK80
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Best and reliable way to annotate genes? Here the genes belong to a assembled phage genome
... Dear Friends, I am trying to annotate genes for a phage genome (Salmonella phagevB SPuM_SP116; Accession: KP010413.1) obtained from a blast hit of an assembled contig. Could you please tell me the best way to do it? I tried DNAmaster but, for some reason it doesn't give me ORF/CDS (predicted by G ...
phages gene annotation dnamaster written 27 days ago by DK80 • updated 27 days ago by natasha.sernova3.3k
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Answer: A: How to include/keep only the samples in a list in VCF.gz file?
... Hi mab658, This issue basically arises when the vcf files are not properly uploaded or dowloaded from the source; could be due to internet issue or some other technical problem. Try to download the file again completely and run the command again. It should work. Deepak ...
written 7 weeks ago by DK80

Latest awards to DK

Popular Question 7 weeks ago, created a question with more than 1,000 views. For AB1 to FASTQ
Centurion 6 months ago, created 100 posts.
Supporter 11 months ago, voted at least 25 times.

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