User: Alec Watanabe
Alec Watanabe • 60
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Posts by Alec Watanabe
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... Hi Mensur,
Assuming we would search for ultraconserved elements in all *Pseudomonas* spp., would you run a global alignment first? If so, would an average computer have enough computation power to handle the high number of genomes? I am familiar with the subsequent steps you mentioned.
Thank you f ...
written 7 months ago by
Alec Watanabe • 60
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... Hi,
A professor asked me to design primers for the detection of *Pseudomonas* spp.. The idea is to detect *Pseudomonas* reads in cancer samples. According to an article, many bacteria could be potentially involved in cancer besides *H. pylori*. I am not sure if designing primers will assure the det ...
written 7 months ago by
Alec Watanabe • 60
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... Thank you. I think this analysis I proposed is extremely intensive both for normal computers and one person. I'm trying another strategy. After reading more about primers (I'm not that familiar with primer design, just know the basics), I think the person who asked me to do this wants a universal pr ...
written 7 months ago by
Alec Watanabe • 60
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... The idea is to use E-value and bit-score to evaluate sequence similarity and then filter out the sequences from the output file. By running BLAST against nt, we could select the non-hit sequences and predict them as *Pseudomonas*-specific. Before that, as I said, we would BLAST PAO1 against the genu ...
written 7 months ago by
Alec Watanabe • 60
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... Just to update this post for anyone who might come across this post.
I'm currently using GET_HOMOLOGUES for pan genome analysis, but mainly for core genome analysis. The graphical output is good and the software can produce ANI and AAI graphs. ...
written 7 months ago by
Alec Watanabe • 60
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... The query is Pseudomonas aeruginosa PAO1 (reference genome). The query will be blasted against the nt database. The idea is that running P. aeruginosa against the Pseudomonas genus will identify sequences within the genus, and running against bacteria (excluding Pseudomonas) will ensure the sequence ...
written 7 months ago by
Alec Watanabe • 60
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... Hi,
First of all, the goal of the analysis is to identify nucleotide sequences exclusive of Pseudomonas. It's a wide range of organisms and I'm aware of that. Unfortunately, the person who asked me to do this did not give me proper instructions or define a specific organism.
Since exclusive nt se ...
written 7 months ago by
Alec Watanabe • 60
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... I think you might be able to use GET_HOMOLOGUES to calculate ANI based on BLAST results. I'm not completely sure as I only calculated ANI for bacteria using this software. The program also prints an image and you can configure the layout of the heatmap. Here is the link if you wanna give it a read a ...
written 10 months ago by
Alec Watanabe • 60
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... Hi Vincent,
I don't have the pathways annotated. I would like to know which pathways are unique to the pathogen (not present in the host) and common (present in both pathogen and host). This investigation constitutes a step of a subtractive proteomics and reverse vaccinology study to identify novel ...
written 10 months ago by
Alec Watanabe • 60
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... Hi,
I want to compare the metabolic pathways of the pathogen (bacteria) with the host (Homo sapiens) using KEGG to find which pathways are common and which are unique to the pathogen. The input file contains fasta sequences with non-host homologous proteins so, in theory, there are no common protei ...
written 10 months ago by
Alec Watanabe • 60
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