User: Bjoux

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Bjoux0
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Posts by Bjoux

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How to calculate the mutual information (MI) between two sites on a protein sequence?
... How to calculate the mutual information (MI) between two sites on a protein sequence? what I need is a standalone tool or python script. Thanks. ...
mutual inforamtion written 3 months ago by Bjoux0 • updated 3 months ago by Jean-Karim Heriche14k
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what is the meaning of 'Species ID' in targetscan?
... what is the meaning of 'Species ID' in targetscan? what is the id of HOMO species? ...
mirna target identification msa targetscan written 10 months ago by Bjoux0 • updated 9 months ago by mirzaei86.vahid10
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How to calcualte the phastCons score of a fake RNA sequence?
... There I have fake RNA seq which is shuffled from a real RNA seq, I want to obtain its phastcons score (conservation score). Apparently, I can not obtain it from UCSC phastcons files. Does someone has ever calculated the PhastCons conservation score and tell me how to get it? Need to obtain an answ ...
phastcons rna-seq ucsc written 13 months ago by Bjoux0
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Comment: C: PhastCons Scores for Human genes (CDS Regions)
... Did you finally find out how to prepare the input files? If you did, please inform me. Thanks !! ...
written 14 months ago by Bjoux0
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Comment: C: How to calculate the conservation score of a short RNA sequence?
... Thanks. I try the approach you mentioned. The procedure is below: 1. dowload the phastCons7way file from UCSC, it contains hg38.phastCons7way.wigFix (17.8GB) which includes the conservation score of each neuleotide. 2.the length of my mrna seq is 1707. the results of mapping this seq to hg38 is: a ...
written 14 months ago by Bjoux0
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Answer: A: Molecular descriptor calculation
... what kind of molecular descriptor do you want to calculate? There are a lot of standard programs such as RDKit and pybel that can calculate many kinds of descriptors. ...
written 14 months ago by Bjoux0
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How to calculate the conservation score of a short RNA sequence?
... I want to calculate the conservation of a segment of RNA sequence (about 50 nt),. I tried phastCons but failed, because I do not know how to prepare the input file. I want to use the download phastcons score of UCSC conservation score file, but I do not have the location of my seq in the genome. Doe ...
conservation ucsc phastcons mirna mirna target written 14 months ago by Bjoux0
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How to calcualte the phastCons score of a short RNA sequence?
... I have a set of 3'UTR mRNA sequence segment, I want to calculate the phastcons score of each nuleotide in the sequence. It is hard to extract the scores from UCSC conservation score files for i do not have the exact location of the sequence in the genome. So I wish to use the phastCons program the ...
alignment phascons rna-seq written 14 months ago by Bjoux0

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