User: nepgorkhey

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nepgorkhey100
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2 years, 3 months ago
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Posts by nepgorkhey

<prev • 14 results • page 1 of 2 • next >
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Answer: A: How to place "\n" after each sequence in a fasta file?
... 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 nepgorkhey100 • updated 3.9 years ago by GenoMax96k
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snp phylogenetics vcf to tree
... 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 ...
vcf phylogenetics snp written 4.0 years ago by nepgorkhey100
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Core genome Multilocus sequence analysis and phylogenetic tree heat map
... 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 ...
genome alignment sequencing written 4.5 years ago by nepgorkhey100
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Answer: A: Finding similar proteins in bacterial genomes
... 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 nepgorkhey100
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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 nepgorkhey100
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Whole genome comparison
... 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.  ...
genome assembly next-gen sequencing written 6.1 years ago by nepgorkhey100
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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 nepgorkhey100
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Single Nucleotide Polymorphisms
... 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 ...
bioinformatics snp written 7.1 years ago by nepgorkhey100 • updated 7.1 years ago by Charles Warden8.0k
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Answer: A: A Quick Way To Annotate Entire Bacterial Genomes To Go?
... 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 nepgorkhey100
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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 nepgorkhey100

Latest awards to nepgorkhey

Popular Question 3.3 years ago, created a question with more than 1,000 views. For Whole genome comparison
Student 3.3 years ago, asked a question with at least 3 up-votes. For snp phylogenetics vcf to tree
Great Question 3.9 years ago, created a question with more than 5,000 views. For Comparison Of Draft Genomes
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Whole genome comparison
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Single Nucleotide Polymorphisms
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Comparison Of Draft Genomes
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Comparison Of Draft Genomes

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