User: Jacob

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Jacob10
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Posts by Jacob

<prev • 33 results • page 1 of 4 • next >
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Obtaining generation times of mammals and reptiles
... I want to find reliable sources that give me the generation time for multiple organisms. This is the average time in years between a parent and it's offspring for an organism. It can also be the age at which an organism reproduces. ...
generation time lifespan written 8 weeks ago by Jacob10
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Answer: A: Giving options to Command line Clustalw
... clustalw < input.txt Where input.txt is 1 file.txt 2 9 4 ^@ 1 ^@ ^@ ^@ X ^@ X The ^@ is one character, not two. It works as the enter key. You can type it like this 1. vim input.txt 2. i #going into insertion mode within vim ...
written 9 weeks ago by Jacob10
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tblastx returning hits with 33% query cover for human genes against the human genome
... I'm running command line tblastx for some human genes as the query sequences against the human genome as the target sequence. Almost all the searches are returning a query cover (qcovhsp) of 33%. I'm thinking that it is no coincidence that amino acids are 3 nucleotides long and that my query covers ...
query cover tblastx blast written 9 weeks ago by Jacob10
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Giving options to Command line Clustalw
... I am trying to run the command line clustalw, but within a loop. Because of this I want to be able to set all the parameters at the time of execution, I don't want to change the parameters manually while the program is running Here is what I am running clustalw 1. Sequence Input From Disc ...
clustalw unix written 9 weeks ago by Jacob10
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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 11 weeks ago by Jacob10 • updated 11 weeks ago by Charles Plessy2.2k
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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 3 months 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 4 months 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 4 months 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 4 months ago by Jacob10 • updated 4 months 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 4 months ago by Jacob10

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