User: DanielC

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DanielC80
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80
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Location:
Canada
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3 days, 7 hours ago
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5 years ago
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Posts by DanielC

<prev • 174 results • page 1 of 18 • next >
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Calculate Ribosome Binding Score for ORFs?
... Dear Friends, I am trying to calculate RBS score for a number of predicted ORFs. I have been researching for a way to do this locally since I have many ORFs. Could you please let me know how this can be done? Thanks for your time. ...
orf rbs written 15 days ago by DanielC80
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Predict the ligand binding site in an Outer Membrane Protein (OMP)?
... Dear Friends, I have the tail fiber proteins of phages that I predicted and annotated. Now, I am trying to find the binding site of these tail fiber proteins in the OMPs of E.Coli LamB receptors. Can you please tell me what steps should I follow to achieve this goal? Thanks much! ...
simulation docking phage tail proteins omp written 19 days ago by DanielC80
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Comment: C: Does Mauve tool work?
... To view mostly, but i think we can manually curate gene annotations there rt? but , it seems to show such errors I mentioned. ...
written 5 weeks ago by DanielC80
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Does Mauve tool work?
... Dear Friends, I have been trying to use Mauve "http://darlinglab.org/mauve/mauve.html". It seems to be showing erros such as, not loading gbk annotations for some files, and not displaying annotations in the "feature" section? I would really appreciate your comments on this and if you know of a bet ...
gene mauve written 5 weeks ago by DanielC80
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Program to align big DNA sequences (100000 bases) and look at conserved regions among them?
... Dear Friends, I have to align 20 DNA sequences of about 100,000 bases each and manually look at a conserved region (tail region; phages) in the alignment to see differences in that region if any. Could you please suggest what tool would be the best for this purpose? As visualization of the region i ...
dna sequence alignment conserved region written 6 weeks ago by DanielC80
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Draw annotations on the predicted CDS/genes using a software/tool
... Dear Friends, I have got phage annotation done using prokka and interproscan (functional annotation). I have the gff files from prokka and interproscan. I am looking to "draw" prokka and interproscan annotations on the predicted CDS/genes on ORF diagram. Could you please tell me any tool to do this ...
assembly genes draw annotation written 6 weeks ago by DanielC80
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Comment: C: Get protein domain information from nucleotide sequence of assembled contigs?
... Thanks for the response! Most of the CDS start with ATG, about 90 to 95%. Moreover, when looking at prokka results, I see that all CDSs start with methionine. To translate, I just used the above command and got translations and didn't have to give any additional parameter for frames. I tried "-meth ...
written 7 weeks ago by DanielC80
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Comment: C: Get protein domain information from nucleotide sequence of assembled contigs?
... OK, I got to translate the CDS sequences to proteins using transeq. However, there is one issue I am facing, not all the starts are translated to methionine and I want to. I used the command: transeq -sequence xx.fasta -outseq yy.fasta -trim -methionine but in the ouptut protein fasta file, I do s ...
written 7 weeks ago by DanielC80
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Comment: C: Get protein domain information from nucleotide sequence of assembled contigs?
... I don't think Glimmer outputs CDS nucleotide and protein fasta file. I am looking for a way to translate the CDSs to proteins standalone. To be honest, not finding any suitable one. Could you please recommend one to me? Thanks! I am tryingto install transeq of EMBOSS but, transeq gives 6 frames and ...
written 7 weeks ago by DanielC80
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Comment: C: Get protein domain information from nucleotide sequence of assembled contigs?
... Thanks! These CDS are predicted by Glimmer. So, if I understand correct, the best approach is to get the CDS translated using EMBOSS (outside from Interproscan)? Then, run Interproscan? And, since I need to do this for many CDS, can this be done locally? Please let me know. Thanks! ...
written 7 weeks ago by DanielC80

Latest awards to DanielC

Popular Question 8 weeks ago, created a question with more than 1,000 views. For Plink1.9 gives error when converting VCF.gz to PED? "Error read failure"
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Find "domains" in a protein sequence
Popular Question 4 months ago, created a question with more than 1,000 views. For AB1 to FASTQ
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Popular Question 6 months ago, created a question with more than 1,000 views. For AB1 to FASTQ
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