User: Alec Watanabe

gravatar for Alec Watanabe
Reputation:
30
Status:
New User
Location:
Last seen:
2 months, 3 weeks ago
Joined:
1 year ago
Email:
a**************@gmail.com

Posts by Alec Watanabe

<prev • 44 results • page 1 of 5 • next >
0
votes
0
answers
157
views
0
answers
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 12 weeks ago by Alec Watanabe30
1
vote
0
answers
157
views
0
answers
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 12 weeks ago by Alec Watanabe30 • updated 9 weeks ago by Biostar ♦♦ 20
0
votes
0
answers
206
views
0
answers
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 Watanabe30
0
votes
1
answer
197
views
1
answers
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 12 weeks ago by Alec Watanabe30
0
votes
1
answer
197
views
1
answer
Can you recommend me a database of bacterial gene essentiality?
... 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 ...
database bacteria essential genes written 3 months ago by Alec Watanabe30 • updated 3 months ago by natasha.sernova3.3k
0
votes
0
answers
206
views
0
answers
Help with whole genome alignment
... 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' ...
alignment help tool written 3 months ago by Alec Watanabe30 • updated 6 weeks ago by Biostar ♦♦ 20
0
votes
1
answer
337
views
1
answer
Best tools for pan genome analysis?
... 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 ...
tools pan genome written 4 months ago by Alec Watanabe30 • updated 4 months ago by jrj.healey10k
1
vote
0
answers
131
views
0
answers
Should we consider unnamed genomospecies in genomic analyses?
... 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 ...
comparative genomics genomospecies written 6 months ago by Alec Watanabe30
0
votes
0
answers
170
views
0
answers
How to apply the reverse vaccinology strategy of Rappuoli?
... 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 ...
reverse vaccinology methodology written 6 months ago by Alec Watanabe30
0
votes
1
answer
303
views
1
answers
Comment: C: Can I upload several Genbank files to RAST?
... 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 Watanabe30

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?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2491 users visited in the last hour