User: Anima Mundi

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Anima Mundi2.5k
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Posts by Anima Mundi

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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 3 days ago by Anima Mundi2.5k
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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 13 days ago by Anima Mundi2.5k
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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 14 days ago by Anima Mundi2.5k
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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 14 days ago by Anima Mundi2.5k
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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 5 weeks ago by Anima Mundi2.5k
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Comment: C: Centrimo error: Template does not contain data section
... Problem solved then, good job ;) ...
written 9 weeks ago by Anima Mundi2.5k
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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 10 weeks ago by Anima Mundi2.5k
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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 10 weeks ago by Anima Mundi2.5k
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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 10 weeks ago by Anima Mundi2.5k
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GenBank entry with apparently unmarked changes
... Dears, I have an mRNA sequence stored as a local file. I retrieved it from GenBank in late 2016 (ID: XM_014915109.1). I just found out that the sequence now appears to be different, but apparently nothing in its GenBank page notifies there were changes after 2016. While it is of course possible tha ...
genbank version update entry item written 11 months ago by Anima Mundi2.5k

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Great Question 13 days ago, created a question with more than 5,000 views. For How To Remove The Comments From A List Of Fasta Sequences
Popular Question 5 weeks ago, created a question with more than 1,000 views. For NCBI is going to eliminate GI identifiers
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Is A Gap At The Same Position In Query And Template Possible?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Is A Gap At The Same Position In Query And Template Possible?
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Great Question 8 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 8 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 9 months 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 11 months ago, created a question with more than 1,000 views. For NCBI is going to eliminate GI identifiers
Popular Question 12 months ago, created a question with more than 1,000 views. For NCBI is going to eliminate GI identifiers
Popular Question 15 months ago, created a question with more than 1,000 views. For Transcriptome Microarray Database
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Epic Question 16 months 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 16 months ago, created a question with more than 10,000 views. For How To Use Bedtools To Extract Promoters From A Mouse Bed File
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Scholar 18 months ago, created an answer that has been accepted. For A: Retrieving RNA sequence from corresponding genomic coordinates
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Popular Question 21 months ago, created a question with more than 1,000 views. For How To Use Bedtools To Extract Promoters From A Mouse Bed File
Popular Question 21 months ago, created a question with more than 1,000 views. For Meme-Suite Is Down... Does Anybody Know What'S Happening?
Popular Question 21 months ago, created a question with more than 1,000 views. For How To Use Bedtools To Extract Promoters From A Mouse Bed File
Popular Question 21 months ago, created a question with more than 1,000 views. For How To Use Bedtools To Extract Promoters From A Mouse Bed File
Great Question 22 months 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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Popular Question 24 months ago, created a question with more than 1,000 views. For How To Use Bedtools To Extract Promoters From A Mouse Bed File

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