Questions tagged [duplications]
The duplications tag has no usage guidance.
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Getting rid of duplicates in a dictionary
I have a tsv file that lists the reads and read lengths from a FASTA file but some reads are duplicated - that's just from the analysis I did previously - but I want to only take one instance of the ...
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How to define an outgroup to build a robust amino acid tree
I building a robust amino acid phylogeny with adequate robustness support (see previous post here).
This is a brief summary of what I have done:
I performed a BLASTp analysis using a protein sequence ...
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How to make a robust amino acid phylogeny with adequate robustness support
This is the second part of this thread: Duplicated genes and genome fragmentation
As @Michael G. suggested, I did a pseudo-annotation of sequences 5-2 and 5-3 (i.e., I joined both sequences into one)...
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Duplicated genes and genome fragmentation [closed]
This is a follow up question to this post: How can I find out if my gene of interest is duplicated?
Briefly, to identify homologous genes, I performed tBLASTn analyses against my genome of interest ...
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How can I find out if my gene of interest is duplicated?
To identify homologous genes, I performed tBLASTn analyses against my genome of interest resulting in sequences of a closely related species. Using this method, I found two (and in some cases up to ...
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How can I locate duplicated regions in a sequence?
I am facing an issue when trying to align short reads against a region in human chr5. The two Sensory Motor Neuron genes, (SMN1 and SMN2) are almost 100% identical and this causes the aligner to fail ...
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How is PCR duplication rate computed in scATAC-seq?
Reading Cusanovich et al. (2015) I encountered the sentence:
We mixed pairs of cell lines (HEK293T or HL-60 versus GM12878), performed combinatorial cellular indexing, and sequenced the resulting ...
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Find paralogs in a draft genome
We generated a (diploid, chordata, highly heterozgous) genome using PacBio and we wanted to see whether it contains lineage-specific duplications (paralogs, basically). The genome is not in Ensembl ...
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