User: Alec Watanabe
Alec Watanabe • 30
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Posts by Alec Watanabe
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... Thank you, I will give it a read today. By the way, E-value should be 1e-05. ...
written 12 weeks ago by
Alec Watanabe • 30
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... 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 ...
written 12 weeks ago by
Alec Watanabe • 30
• updated
9 weeks 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 12 weeks ago by
Alec Watanabe • 30
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... 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 12 weeks ago by
Alec Watanabe • 30
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... Hi, I'm analyzing 50+ complete genomes of Enterococcus faecium and have extracted the core genome of these sequences. Now I want to narrow down the core genome sequences by searching essential genes for these bacteria. Searching on the web, I've found DEG, CEG and OGEE, DEG being the most appropriat ...
written 3 months ago by
Alec Watanabe • 30
• updated
3 months ago by
natasha.sernova • 3.3k
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... Hello. I am looking for a tool or a methodology to make whole genome alignments with 50+ genomes. I used to use Gegenees that basically construct a matrix (heatmap) of similarity based on all vs all BLAST results. Recently, Gegenees stopped working and I don't know the reason. It might be because I' ...
written 3 months ago by
Alec Watanabe • 30
• updated
6 weeks ago by
Biostar ♦♦ 20
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... Hi, I'm working with more than a 100 bacterial genomes of Proteus and want to do a pan genome analysis of the genus. I'm currently using Prokka to annotate genomes which were downloaded from the NCBI and Roary will be used for the pan genome analyses. I want to know if:
1. these softwares are rel ...
written 4 months ago by
Alec Watanabe • 30
• updated
4 months ago by
jrj.healey ♦ 10k
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... Hi,
As the title says, should we include unnamed genomospecies in comparative genomics analyses, reverse vaccinology, CRISPR prediction, etc? (i.e. prediction of pan genome, core genome, accessory genome, etc).
I read that the "Report of the ad hoc committee on reconciliation of approaches to bact ...
written 6 months ago by
Alec Watanabe • 30
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... Greetings,
I have been working with reverse vaccinology of Rappuoli but only with a few genomes, thus the amount of data I have to analyze is small. Now I want to analyze a considerable number of genomes (more than 100). Do you have any suggestions on how to predict genomic islands (PAIs, RIs, SIs ...
written 6 months ago by
Alec Watanabe • 30
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... Thanks for your reply! I've been reading about the command line option of RAST and it will for sure facilitate the process shall I use it. If I were to switch to prokka, do you recommend any software for pan-genome analysis? I'd need to test it, but I'm not completely sure that PanWeb would accept t ...
written 6 months ago by
Alec Watanabe • 30
Latest awards to Alec Watanabe
Scholar
12 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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