User: Alec Watanabe

gravatar for Alec Watanabe
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Posts by Alec Watanabe

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Comment: C: average nucleotide identity (ani) of fungi
... 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 weeks ago by Alec Watanabe30
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Comment: C: Comparing the metabolic pathways of pathogen and host using KEGG?
... 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 weeks ago by Alec Watanabe30
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Comparing the metabolic pathways of pathogen and host using KEGG?
... 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 ...
drug targets methodology kegg written 11 weeks ago by Alec Watanabe30
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Doubts about a subtrative proteomics approach adopted in an article
... Hello, The following article https://www.nature.com/articles/s41598-018-26689-7#Sec28 under the section Methods subsection Pathogen-specific pathways explains how the researches identified proteins only present in pathogen pathways. I am quite confused about the methodology here. Apparently, they l ...
proteomics subtractive methodology written 11 weeks ago by Alec Watanabe30
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Comment: C: How to obtain a list of proteins involved in organism specific pathways?
... I'd love to. It seems like PathBLAST is a great tool. Unfortunately, the amount of queries that I have makes the tool, in its actual state, a little challenging. The FAQ section does mention a downloadable version of PathBLAST but its not implemented yet. Hopefully, soon we will have the chance to t ...
written 12 weeks ago by Alec Watanabe30
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How to obtain a list of proteins involved in organism specific pathways?
... Hello Biostars community, I know there are some posts about pathways, KEGG and other tools but I do not quite think it is the same solution for me. Lets say I have a multifasta file containing protein sequences. What I want to do is analyze this set of proteins against an organism specific pathway ...
pathways written 12 weeks ago by Alec Watanabe30
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Comment: C: Help me with BLAST pairwise alignment parameters
... Thank you, I will give it a read today. By the way, E-value should be 1e-05. ...
written 7 months ago by Alec Watanabe30
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Help me with BLAST pairwise alignment parameters
... Hi, if I were to run BLAST pairwise alignments to find sequence similarities as the initial step for protein clustering, just like other softwares employ for pan genomic analyses, would a 75% coverage provide me with significant matches given that I'm working with genomes with 92%+ similarity? Is th ...
parameters blast pairwise alignment written 7 months ago by Alec Watanabe30 • updated 6 months ago by Biostar ♦♦ 20
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Comment: C: Help with whole genome alignment
... Thank you for all the answers. Just to provide a feedback, searching on the web I ended up finding about GET_HOMOLOGUES which can be used to create pan genome matrices thus fitting what I needed. ...
written 7 months ago by Alec Watanabe30
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Comment: C: Can you recommend me a database of bacterial gene essentiality?
... Really interesting ideas that you brought. Gave a quick read on the article and apparently OGEE is the only database available at the moment. Technically one can take the list of essential genes and screen against the desired database. Besides the databases, the screening of essential genes given th ...
written 7 months ago by Alec Watanabe30

Latest awards to Alec Watanabe

Scholar 16 months ago, created an answer that has been accepted. For A: How can I convert an EMBL file into a multiFASTA file?

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