User: DanielC

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DanielC100
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Canada
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Posts by DanielC

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Comment: C: Crystal structure of lambda phage?
... No, i will see if lambda phage sequence can be found, any idea on this? once we have the sequence we do blast against pdb database; is this what you mean?Thanks ...
written 12 days ago by DanielC100
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Comment: C: Crystal structure of lambda phage?
... Thanks! I am looking for the tail fiber structure of the lambda phage. Could you please let me know about your suggestions on this? ...
written 12 days ago by DanielC100
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Comment: C: how many genomes from BLAST hit should be considered for phylogeny tree analysis
... Thanks! I have performed gene level (using terminase subunit of the genomes) and generated tree from that. Do you think that analysis is considerably OK to predict the family or order the assembled genome belong to? I am working on phages. or use mash distances as a surrogate for sequence iden ...
written 12 days ago by DanielC100
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Comment: C: how many genomes from BLAST hit should be considered for phylogeny tree analysis
... All validations are done for the assembled genome and it is significantly accurate. Regarding the other genomes from the BLASTn hit, i cannot say, but the sequence identity and query coverage is > 92% for most of the BLAST hits. Also, that is not the concern for me at the moment. Could you please ...
written 12 days ago by DanielC100
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how many genomes from BLAST hit should be considered for phylogeny tree analysis?
... Dear Friends, I am trying to perform phylogeny analysis on an assembled genomes. From BLASTn searchI got 250 genomes. I am looking to generated phylogeny tree using these genomes and the assembled genome. However, all programs I have used till now like, Mugsy, Clustal Omega, Mafft, failed in produc ...
phylogeny genome taxonomy tree written 12 days ago by DanielC100 • updated 2 days ago by Biostar ♦♦ 20
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Comment: C: Crystal structure of lambda phage?
... Thanks! Yes, I did, there are quite a few, but I am not sure which structure is the one of Lamda phage for E-Coli. Do you have any idea if there is one? Thanks! ...
written 13 days ago by DanielC100
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Crystal structure of lambda phage?
... Dear Friends, Can you please let me know if there is crystal structure available for "Lambda phage"? I would really appreciate if you could let me know the PDB of it. Thank you for your time. ...
lambda phage e-coli written 13 days ago by DanielC100
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Comment: C: How to performs genome assembly of multiple phages in one Fastq single-end file?
... thanks for the response! No, the phages are isolated from water taken from different locations. I dont know if it possible to detect the phage type from merely this information. Since, we dont know what phage it could belong to, what would you suggest would be an efficient strategy to perform ge ...
written 18 days ago by DanielC100
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How to performs genome assembly of multiple phages in one Fastq single-end file?
... Dear Friends, I have a FASTq file with reads from multiple phages. Could you please let me know how to extract and perform genome assembly of every phage in this fastq file? I have the experience of performing genome assembly on one phage in one FASTQ file but not for multiple phages in a fastq fil ...
genome assembly fastq written 18 days ago by DanielC100
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Comment: C: Calculate Ribosome Binding Score for ORFs?
... Thanks! I ran this but, gave this error: python ../RBS_Calculator.py contig.fasta Cutoff = 10 Traceback (most recent call last): File "../RBS_Calculator.py", line 1085, in handle = open(filename,"rU") IOError: [Errno 2] No such file or directory: '/common/RBS_Calcul ...
written 23 days ago by DanielC100

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