User: Jacob
Jacob • 0
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Posts by Jacob
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... I don't know what that means, I'm trying make an accurate estimate of tumour stage based on a bunch of other data I have so that I can compare patient data where tumour stage is know to other data where tumour stage is not known ...
written 8 days ago by
Jacob • 0
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... For template_type and template_length, this is all I can really find on them
-template_type
Discontiguous MegaBLAST template type
-template_length
Discontiguous MegaBLAST template length
I don't really know what they are though and I don't know what differences setting op ...
written 9 days ago by
Jacob • 0
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... I'm working with breast cancer data and have lots of patient information regarding the tumour size(in cm), the type of the tumour(invasive ductal carcinoma; invasive lobular carcinoma; inflammatory carcinoma), the presence of lymph node metastasis, age of the patient, etc. For some patients I have i ...
written 13 days ago by
Jacob • 0
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13 days ago by
jmzeng1314 • 0
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... I'm performing blast searches with only exon regions for certain genes against various genomes(for different organisms).
For example, I will blast regions 1..367, 368..444, 445..828 of the gene ACAN(https://www.ncbi.nlm.nih.gov/nuccore/NM_013227.3) against an organisms genome such as
ftp://ftp ...
written 14 days ago by
Jacob • 0
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... Do you know the reasoning behind the numbering? It looks like within `genomes/all/GCF/000/001/` there is only humans chimpanzees and some similar rodents (all genomes that likely have been sequenced a lot). Is there some type of pattern or technique to the path organization? ...
written 15 days ago by
Jacob • 0
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... I am getting some genomes from the ncbi ftp site, one of the genomes(Mus musculus) is
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.25_GRCm38.p5/GCF_000001635.25_GRCm38.p5_genomic.fna.gz
I'm wondering what the `GCF/000/001/635` in the path name means. What do GCF, 000, 0 ...
written 15 days ago by
Jacob • 0
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15 days ago by
Devon Ryan ♦ 68k
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... I'm able to get the genbank file from the website and print the features from the file, but I want to only print the features where type='exon'. Further, I want print just the Exactposition fields for those features where type='exon'
heres what I am doing so far
>>> handle = Entrez.efe ...
written 20 days ago by
Jacob • 0
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20 days ago by
a.zielezinski ♦ 7.0k
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... Is there a way to get all the exon regions from that website using a command line tool? ...
written 21 days ago by
Jacob • 0
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... I want to use some type of e-utility tool to obtain the fasta mRNA sequence file of a gene.
First I'm getting the uid from Gene with the code below
from Bio import Entrez
Entrez.email="email@address.com
handle = Entrez.esearch(db="gene", term="Acan[Gene Name] AND Homo sapiens[Organism] ...
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... I kind of found an answer to this question here "https://www.biostars.org/p/121972/" but it's not very clear to me and they don't explain qcovus. Which one would be the one I probably want if I want to find out how much of my query sequence is within an organisms genome. What is meant by overlap inf ...
written 23 days ago by
Jacob • 0
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