User: Jacob
Jacob • 10
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- 10
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- New User
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- Last seen:
- 2 weeks, 1 day ago
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- 3 months, 1 week ago
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Posts by Jacob
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... 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 ...
written 17 days ago by
Jacob • 10
• updated
16 days ago by
Charles Plessy • 2.1k
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... 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
Jacob • 10
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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 9 weeks ago by
Jacob • 10
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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 weeks ago by
Jacob • 10
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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 10 weeks ago by
Jacob • 10
• updated
10 weeks ago by
jmzeng1314 • 20
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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 10 weeks ago by
Jacob • 10
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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 10 weeks ago by
Jacob • 10
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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 10 weeks ago by
Jacob • 10
• updated
10 weeks ago by
Devon Ryan ♦ 70k
2
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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 11 weeks ago by
Jacob • 10
• updated
11 weeks ago by
a.zielezinski ♦ 7.2k
0
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... Is there a way to get all the exon regions from that website using a command line tool? ...
written 11 weeks ago by
Jacob • 10
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