User: Anima Mundi

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Anima Mundi2.8k
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Posts by Anima Mundi

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Comment: C: Genome aligner that shows annotations too
... Hi, you may try MacVector, SnapGene or VectorNTI (actually, the latter has been [recently discontinued][1]). [1]: https://www.thermofisher.com/it/en/home/life-science/cloning/vector-nti-software.html ...
written 12 months ago by Anima Mundi2.8k
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Comment: C: Distinguish between homo- or heterozygote alleles if you sequence for a gene
... Hi myrrlicht, the explanation is already found above. If you have gone for the electropherogram-based method and observed a few double peaks on a single exon (not exome, which is a different thing!) then no other action is needed. If you want to understand the exact sequence of each variant of the ...
written 15 months ago by Anima Mundi2.8k
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Comment: C: Distinguish between homo- or heterozygote alleles if you sequence for a gene
... Of course the approach gives for granted that you have some pre-existing knowledge about the alleles you are talking about. For instance, say that you have a gene with two **known** alleles, differing for a few nucleotides in a given position. You would design primers on constant regions across this ...
written 15 months ago by Anima Mundi2.8k
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Comment: C: Distinguish between homo- or heterozygote alleles if you sequence for a gene
... It all depends on your pipeline I would say: typically you would use Sanger-related methods for low-throughput projects, with procedures alike those exemplified above. In NGS-based workflows you would more likely get reads from all alleles present in your initial sample. In your shoes, probably I w ...
written 15 months ago by Anima Mundi2.8k
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Answer: A: Distinguish between homo- or heterozygote alleles if you sequence for a gene
... Hi, if you are talking about Sanger sequencing (and the like) you need to extract genomic DNA, amplify a portion of the gene and clone it. Then you should transform competent bacteria and screen some of the resulting colonies. If the sample is heterozygote for the gene, you will have two different a ...
written 15 months ago by Anima Mundi2.8k
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Comment: C: Why could we infer a physical time scale (e.g. a billion year) from a phylogenet
... Yes, these are called "calibration fossils". ...
written 16 months ago by Anima Mundi2.8k
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Comment: C: Centrimo error: Template does not contain data section
... Problem solved then, good job ;) ...
written 17 months ago by Anima Mundi2.8k
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Comment: C: Centrimo error: Template does not contain data section
... Mmm, I see. Using the Jaspar database I suggested on your minimal example fixes the problem? And using uniprobe_mouse.meme only? ...
written 17 months ago by Anima Mundi2.8k
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Answer: A: Centrimo error: Template does not contain data section
... Hi again, I see what is causing the error. It looks like your database `JASPAR2018_CORE_vertebrates_non-redundant.meme` needs some reformatting. For each motif you provided, I just truncated header line, setting `letter-probability...` as a second line, *i.e.*: MEME version 4 ALPHABET ...
written 17 months ago by Anima Mundi2.8k
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Comment: C: Centrimo error: Template does not contain data section
... Hi, not sure if this might help you. A quick-and-dirty version of your command yields an output without problems for me, albeit with no enriched motifs for the sample sequences you provided. Here is what I tried: `centrimo --oc centrimo_out --verbosity 1 --score 5.0 --ethresh 10.0 --bfile Cluster_7. ...
written 17 months ago by Anima Mundi2.8k

Latest awards to Anima Mundi

Epic Question 5 months ago, created a question with more than 10,000 views. For How To Use Bedtools To Extract Promoters From A Mouse Bed File
Popular Question 8 months ago, created a question with more than 1,000 views. For NCBI is going to eliminate GI identifiers
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Is A Gap At The Same Position In Query And Template Possible?
Good Question 8 months ago, asked a question that was upvoted at least 5 times. For How To Use Bedtools To Extract Promoters From A Mouse Bed File
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Should Fasta Be Capitalized?
Great Question 11 months ago, created a question with more than 5,000 views. For How To Remove The Comments From A List Of Fasta Sequences
Scholar 12 months ago, created an answer that has been accepted. For A: Retrieving RNA sequence from corresponding genomic coordinates
Scholar 14 months ago, created an answer that has been accepted. For A: Retrieving RNA sequence from corresponding genomic coordinates
Great Question 15 months ago, created a question with more than 5,000 views. For How To Remove The Comments From A List Of Fasta Sequences
Popular Question 16 months ago, created a question with more than 1,000 views. For NCBI is going to eliminate GI identifiers
Appreciated 16 months ago, created a post with more than 5 votes. For A: Is A Gap At The Same Position In Query And Template Possible?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Is A Gap At The Same Position In Query And Template Possible?
Appreciated 23 months ago, created a post with more than 5 votes. For A: Is A Gap At The Same Position In Query And Template Possible?
Great Question 23 months ago, created a question with more than 5,000 views. For How To Use Bedtools To Extract Promoters From A Mouse Bed File
Great Question 23 months ago, created a question with more than 5,000 views. For How To Use Bedtools To Extract Promoters From A Mouse Bed File
Student 2.0 years ago, asked a question with at least 3 up-votes. For How To Use Bedtools To Extract Promoters From A Mouse Bed File
Popular Question 2.2 years ago, created a question with more than 1,000 views. For NCBI is going to eliminate GI identifiers
Popular Question 2.3 years ago, created a question with more than 1,000 views. For NCBI is going to eliminate GI identifiers
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Transcriptome Microarray Database
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Transcriptome Microarray Database
Epic Question 2.6 years ago, created a question with more than 10,000 views. For How To Use Bedtools To Extract Promoters From A Mouse Bed File
Epic Question 2.6 years ago, created a question with more than 10,000 views. For How To Use Bedtools To Extract Promoters From A Mouse Bed File
Popular Question 2.7 years ago, created a question with more than 1,000 views. For How To Download All The Introns From Ensembl
Scholar 2.8 years ago, created an answer that has been accepted. For A: Retrieving RNA sequence from corresponding genomic coordinates
Great Question 3.0 years ago, created a question with more than 5,000 views. For How To Use Bedtools To Extract Promoters From A Mouse Bed File

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