User: microfuge

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microfuge1.5k
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Posts by microfuge

<prev • 257 results • page 1 of 26 • next >
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Comment: C: How to get the nucleotide sequence of all strains of a virus in NCBI?
... Once way to use NCBI Taxonomy. For example putting "Dengue virus" here https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi and clicking assemblies radio button "assemblies" gives 6 . ...
written 15 days ago by microfuge1.5k
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Comment: C: Retrieve GFF3 file from ncbi
... Nice Solution to this problem! ...
written 6 weeks ago by microfuge1.5k
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Comment: C: What makes certain genomes harder to sequence? Are there any trends among taxono
... NCBI taxonomy can be potentially used to get such trends. Something like for each clade get the fraction of species with an available genome. Will try to give it a try. ...
written 8 weeks ago by microfuge1.5k
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Comment: C: nucleotide substitution model
... I could be wrong but rate heterogeneity is typically for variation in mutation rate across genome. The mutation rate itself is a distribution as it varies (usually modelled as a gamma distribution). ...
written 9 weeks ago by microfuge1.5k
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Comment: C: Useful productivity tools for bioinformaticians
... I would highly recommend this book "wicked cool shell scripts" https://nostarch.com/wicked2 . One of my favorites from the book is the command line notepad . Most times you are on the terminal and want to write a quick note without moving, it can be easily done with the note shell script. note . ...
written 9 weeks ago by microfuge1.5k
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Comment: C: Obtain N50 stats from NCBI for all Hymenoptera genome assemblies
... Really liked this solution! ...
written 12 weeks ago by microfuge1.5k
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Comment: C: how can i find all of genes involve in special disease?
... If genes are from a particular species only this can be done with biomart * Go to ensembl biomart https://www.ensembl.org/biomart/martview/31624ea7ad77f20bf544e31b22268447 * Select human genes * In Filters tab on the left side expand phenotype tab * Scroll down the list to get to phenotype/disea ...
written 12 weeks ago by microfuge1.5k
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Comment: C: How to calculate GC% at 1st, 2nd and 3rd codon position for each sequence in a m
... A blast from the past but codonw calculates per sequence GC3 and many other stats directly from the CDS fasta file http://codonw.sourceforge.net/#Downloading%20and%20Installation . ...
written 12 weeks ago by microfuge1.5k
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Comment: C: Obtain N50 stats from NCBI for all Hymenoptera genome assemblies
... I always find convinient to start with NCBI Taxonomy. One approach can be - - In NCBI taxonomy https://www.ncbi.nlm.nih.gov/taxonomy enter Hymenoptera in search box - Click on resulting link which opens this page https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7399 - Check the Genome ...
written 12 weeks ago by microfuge1.5k
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Comment: C: Is there a database with calculated Ka/Ks ratios for human/mouse genomes?
... It does provides ka/ks values in Attribute -> Homologous (radio button) -> Orthologs -> scroll down to locate species (mouse) -> radio buttons (dn with mouse and ds with mouse) ...
written 3 months ago by microfuge1.5k

Latest awards to microfuge

Teacher 5 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Voter 5 months ago, voted more than 100 times.
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Scholar 11 months ago, created an answer that has been accepted. For C: BedTools getfasta -split
Guru 11 months ago, received more than 100 upvotes.
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 20 months ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 20 months ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 20 months ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Scholar 21 months ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Commentator 23 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Tissue Specificity index (tau) should FPKM data be log transformed?
Scholar 2.5 years ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 2.6 years ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Scholar 2.6 years ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: chain file for maize
Commentator 3.4 years ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
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Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: chain file for maize
Centurion 3.4 years ago, created 100 posts.

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