User: Monika515

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Monika5150
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Posts by Monika515

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Common Newick Trees with "proximities" for use with PhyloGibbs
... The program PhyloGibbs available for use: http://www.phylogibbs.unibas.ch/cgi-bin/phylogibbs.pl has a requirement for a species tree in newick format where the numbers do not correspond to branch length but proximity to common ancestor defined as " A proximity gives the probability that no mutation ...
gene alignment regulation sequence promoter written 2.1 years ago by Monika5150
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In RSAT retrieve_Ensembl_seq do FASTA sequences of genes on reverse strands take this into account?
... I am retrieving some orthologous promoter regions relative to the mRNA, some of the reference genes are on the reverse strand. What I want to know is if the retrieved FASTA sequence is of the reverse strand and is it flipped 3' to 5' so that the gene code can be read left to right, or if the default ...
sequence written 2.1 years ago by Monika5150
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How to write code to extract e.g. 1kb upstream of desired sequence to obtain promoter sequences for analysis?
... I will be working with a specific human gene (let's call it X), for which I am to predict possible transcription factors. For this I want to work with the promoter sequences instead of the actual gene sequences. I am familiar with how to extract sequences in Biopython. I am rather new to coding and ...
gene sequence written 2.3 years ago by Monika5150 • updated 2.3 years ago by Nicolas Rosewick8.8k

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