User: zuhaibzulfiqarahmed

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Posts by zuhaibzulfiqarahmed

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Comment: C: Relation between GO terms of homologous genes in different organisms.
... Thank You! The way I was thinking of doing it is to pool all the GO terms from all results, and take the top 3 or 4, as a representative annotation for the gene. For example, for the mgsA gene has results in cows, humans, myobacterium, sacchromyces, etc. So take all the GO annotations from all those ...
written 4 weeks ago by zuhaibzulfiqarahmed0
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Comment: C: Relation between GO terms of homologous genes in different organisms.
... @Jean-Karim Heriche Thanks for the reply. So for example, the mgsA gene in E coli would have similar annotations as the mgsA gene in humans? ...
written 5 weeks ago by zuhaibzulfiqarahmed0
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Relation between GO terms of homologous genes in different organisms.
... Hello, I'm writing a small program that takes in a list of Uniprot gene names (and organisms of interest), and returns a visual representation of the GO terms associated with that list of genes in the specified organisms. I've run into an issue though. What if Uniprot doesn't have the GO terms for ...
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Is Prokka giving me an inaccurate number of genes?
... Hello, So I'm using Prokka to annotate the Borrelia Burgdorferi reference genome (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/008/685/GCF_000008685.2_ASM868v2) So once I ran prokka on the .fna file, I used the following command to get the list of genes #Gets the list of genes, and puts th ...
software error annotation prokka gene assembly written 12 weeks ago by zuhaibzulfiqarahmed0 • updated 12 weeks ago by h.mon23k
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Comment: C: How to Determine Which Bacterial Assembly to Use from NCBI database?
... Thank You. But is it safe to assume that the newest assembly is the most accurate one? I'd actually like to explore what sort of genes are on the plasmid, but some assemblies only show one chromosome. So should I go for another assembly? ...
written 3 months ago by zuhaibzulfiqarahmed0
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How to Determine Which Bacterial Assembly to Use from NCBI database?
... Hello, I'm working on a final project for my genomics course. I'd like to analyze the genomes for a few species of Borrelia. However, the assemblies of the genomes seem to be very inconsistent. For example, for Borrelia afzelii, one assembly has 6 chromosomes and plasmids, and another has 10. Anoth ...
ncbi assembly written 3 months ago by zuhaibzulfiqarahmed0

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