User: Jacob

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Jacob10
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Posts by Jacob

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Using needle command with no output to the terminal
... I'm am using the needle command and would just like there to be no output to the terminal For example this is what I run needle -asequence seq1.fna -bsequence seq2.fna -gapopen 0 -gapextend 2 -outfile file.needle Needleman-Wunsch global alignment of two sequences And I would jus ...
silent needle emboss written 17 days ago by Jacob10 • updated 16 days ago by Charles Plessy2.1k
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Comment: C: Is there a program that can predict or accurately guess tumour stage from inform
... No just if theres a program that can take in this data and decide the stage, because I'm worried about misclassifying the stage based on my level of understanding. ...
written 7 weeks ago by Jacob10
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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 9 weeks ago by Jacob10
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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 weeks ago by Jacob10
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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 10 weeks ago by Jacob10 • updated 10 weeks ago by jmzeng131420
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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 10 weeks ago by Jacob10
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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 10 weeks ago by Jacob10
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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 10 weeks ago by Jacob10 • updated 10 weeks ago by Devon Ryan70k
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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 11 weeks ago by Jacob10 • updated 11 weeks ago by a.zielezinski7.2k
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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 11 weeks ago by Jacob10

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