User: Jacob

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Jacob0
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Posts by Jacob

<prev • 27 results • page 1 of 3 • next >
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Comment: C: Is there a program that can predict or accurately guess tumour stage from inform
... 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 Jacob0
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What do the blast parameters template_type, template_length, best_hit_overhang, and best_hit_score_edge do
... 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 ...
discontiguous-megablast blast written 9 days ago by Jacob0
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Is there a program that can predict or accurately guess tumour stage from information like tumour size, type, presence of lymph node metastasis etc
... 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 ...
tumour stage machine learning cancer written 13 days ago by Jacob0 • updated 13 days ago by jmzeng13140
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Receiving low query covers for blast searches on genome files, but not transcript files
... 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 ...
genome blast transcript rna-seq written 14 days ago by Jacob0
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Comment: C: Meaning behind the path organization in NCBI ftp site
... 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 Jacob0
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Meaning behind the path organization in NCBI ftp site
... 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 ...
ncbi genome ftp written 15 days ago by Jacob0 • updated 15 days ago by Devon Ryan68k
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Printing features of a specific type only from a Genbank file with Biopython
... 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 ...
seq biopython genbank seqio written 20 days ago by Jacob0 • updated 20 days ago by a.zielezinski7.0k
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Comment: C: Using efetch(biopython) to get the fasta file of an mRNA, as well as the exon lo
... Is there a way to get all the exon regions from that website using a command line tool? ...
written 21 days ago by Jacob0
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Using efetch(biopython) to get the fasta file of an mRNA, as well as the exon locations
... 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] ...
python efetch biopython entrez written 21 days ago by Jacob0 • updated 21 days ago by Ben40
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What is the difference between qcovs, qcovhsp, qcovus in blast
... 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 ...
blast qcov written 23 days ago by Jacob0

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