User: Mohak

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Mohak0
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Posts by Mohak

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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 6 months ago by Mohak0 • updated 6 months ago by Devon Ryan74k
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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 11 months 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 11 months ago by Mohak0 • updated 11 months ago by Lina F110
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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 13 months ago by Mohak0

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