User: Mohak

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Mohak0
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Posts by Mohak

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NCBI Taxon ID to IMG Genome IDs
... I have a bunch of NCBI taxon IDs and I want to find there IMG genome IDs. I can try HTML parsing, but the link I get when I type a particular ncbi taxon ID is not unique. For example, when i search for ncbi taxon id 115711, i get the following link opened https://img.jgi.doe.gov/cgi-bin/m/main. ...
bioinformatics parsing html parsing ids written 12 weeks ago by Mohak0
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Genome size statistical analysis
... I am looking at the patterns of distribution of a particular pair of genes in bacteria. One of the characteristics that I am studying is genome size. What I found is that organisms having this gene pair tend to have significantly (Wilcoxon rank sum test) higher genome sizes as compared to organisms ...
bioinformatics genomics statistics written 16 months ago by Mohak0
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Error while running MEGAX
... I am running the latest version of MEGA i.e MEGAX. I am trying to run the command megacc but it is throwing an error. My sequences.fas file contains the trimmed multiple sequence alignment (MSA) of 16S rRNA sequences of 1403 organisms in a fasta format. This file was generated after running MUSCLE ...
multiple sequence alignment megax written 16 months ago by Mohak0
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Concatenating alleles at detected sites to form fasta sequences from vcf files
... I have a multi-vcf file with various samples of a bacterial genome, in the following format, NC_num 20 . A T 66 . DP=1850;VDB=0.015032;SGB=16.4938;RPB=0.0719749;MQB=0.782089;MQSB=0.998951;BQB=0.976407;MQ0F=0;AC=1;AN=32;DP4=1599,229,6,0;MQ=59 GT:PL 0:0,255 ...
vcf sequence alignment msa snp written 2.4 years ago by Mohak0 • updated 2.4 years ago by Devon Ryan92k
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Comment: C: Classification of bacteria - bioinformatics
... Thanks Lina! I wasn't aware of the KEGG tree. Beautifulsoup solves the problem! And never used the eUtils API, but the biopython link seems useful. Will definitely try that out. Thanks a ton! :) ...
written 2.8 years ago by Mohak0
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Classification of bacteria - bioinformatics
... I want to do an enrichment analysis across all bacterial phyla/classes. For this I first need to know, of all the genomes I have in my database, how many of them are gammaproteobacteria, spirochetes etc. A list which gives the names of these bacteria, their type and their accession number. Is there ...
genome accession numbers type of bacteria written 2.8 years ago by Mohak0 • updated 2.8 years ago by Lina F160
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Protein secondary structure prediction
... I carried out an SNP analysis on a dataset and found few critical SNPs across various proteins. After filtering for these critical SNPs I found the domains in which they lie. Now next what I want to do is incorporate those SNPs (let's say one SNP per protein sequence) and see where and if they lie i ...
snp secondary structure prediction written 2.9 years ago by Mohak0

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