User: Mohak

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Mohak0
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Posts by Mohak

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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 9 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 9 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 21 months ago by Mohak0 • updated 21 months ago by Devon Ryan88k
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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 2.2 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 2.2 years ago by Mohak0 • updated 2.2 years ago by Lina F150
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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 2.4 years ago by Mohak0

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