User: nepgorkhey
nepgorkhey • 100
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Posts by nepgorkhey
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2
votes
2
answers
912
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2
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... a short python script like the following may work for you
for lines in f:
if lines[0]=='>':
print lines
else:
lines=lines+'\n'
print lines ...
written 3.9 years ago by
nepgorkhey • 100
• updated
3.9 years ago by
GenoMax ♦ 96k
4
votes
0
answers
2.4k
views
0
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... Hi All,
I identified SNPs from about 60 bacterial genomes using GATK and the same reference genome was used throughout. I currently have separate VCF files with SNPs for each bacterial genome. My main goal is to construct a maximum likelihood phylogenetic tree using these SNPs. I am now kind of st ...
written 4.0 years ago by
nepgorkhey • 100
0
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1.2k
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... I wanted to make a phylogenetic tree using core genes from a number of bacterial strains. For this I had approximately 100 genomes, I used the annotated sequences and using a python script, I narrowed down the core genes for my 100 genomes. In the output, I got around 500 files, each file with a gen ...
written 4.5 years ago by
nepgorkhey • 100
0
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3
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1.5k
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3
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... You can use get_homologues software for that. Works fine if you have both amino acid and nucleotide sequences.
...
written 4.7 years ago by
nepgorkhey • 100
0
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2
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2.0k
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Answer:
A: Whole genome comparison
... Seems like get_homologues is going to help me...Thanks a lot :)
...
written 6.1 years ago by
nepgorkhey • 100
2
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2
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2.0k
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2
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... During comparative genome analysis, how will it be possible to extract similar genes and their sequences from two whole genomes? Suppose, when working with two bacteria genomes we found they have 3500 genes in common. Now I want to take the sequences of those 3500 genes from both the genomes.
...
written 6.1 years ago by
nepgorkhey • 100
0
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3
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1.7k
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3
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Comment:
C: Single Nucleotide Polymorphisms
... I am working with Xanthomonas bacteria and the database has no SNP data.
...
written 7.0 years ago by
nepgorkhey • 100
6
votes
3
answers
1.7k
views
5 follow
3
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... Hi,
I am working with whole genome sequences of bacteria and want to identify SNPs from the genomes for each sequences. What would be the best way to identify these SNPs that will allow me to compare the variation between them.
Thanks a lot.
Sujan
...
written 7.1 years ago by
nepgorkhey • 100
• updated
7.1 years ago by
Charles Warden ♦ 8.0k
1
vote
3
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6.9k
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3
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... I guess you can use JGI IMG platform to annotate your bacterial genomes by uploading your sequences in their database. You can still keep your sequences private if you don't want other to use it.
...
written 7.1 years ago by
nepgorkhey • 100
0
votes
1
answer
7.7k
views
1
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Comment:
C: Comparison Of Draft Genomes
... Thanks a lot. I will definitely try your suggestions. The thing with MAUVE is that, as i was using draft genomes it showed lot of interconnections between the genomes. It was showing lot of rearrangements between the genomes that I was trying to look for but had lot of interconnecting lines showing ...
written 7.1 years ago by
nepgorkhey • 100
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For Whole genome comparison
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3.9 years ago,
created a question with more than 5,000 views.
For Comparison Of Draft Genomes
Popular Question
3.9 years ago,
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For Whole genome comparison
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3.9 years ago,
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For Single Nucleotide Polymorphisms
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For Comparison Of Draft Genomes
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For Comparison Of Draft Genomes
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