User: Jacob

gravatar for Jacob
Jacob10
Reputation:
10
Status:
New User
Location:
Last seen:
8 months ago
Joined:
11 months, 2 weeks ago
Email:
s*****************@gmail.com

Posts by Jacob

<prev • 33 results • page 1 of 4 • next >
2
votes
0
answers
302
views
0
answers
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 months ago by Jacob10
0
votes
1
answer
451
views
1
answers
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 8 months ago by Jacob10
0
votes
0
answers
274
views
0
answers
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 8 months ago by Jacob10
0
votes
1
answer
451
views
1
answer
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 8 months ago by Jacob10
3
votes
1
answer
344
views
1
answer
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 8 months ago by Jacob10 • updated 8 months ago by Charles Plessy2.4k
0
votes
1
answer
372
views
1
answers
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 10 months ago by Jacob10
0
votes
1
answer
372
views
1
answers
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 10 months ago by Jacob10
0
votes
0
answers
305
views
0
answers
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 10 months ago by Jacob10
0
votes
1
answer
372
views
1
answer
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 months ago by Jacob10 • updated 5 months ago by Biostar ♦♦ 20
0
votes
0
answers
315
views
0
answers
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 months ago by Jacob10

Latest awards to Jacob

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1166 users visited in the last hour