User: microfuge

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microfuge720
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Posts by microfuge

<prev • 165 results • page 1 of 17 • next >
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Comment: C: fasta redundant sequence
... If it is ok for you to run legacy blast then this link could be of use https://www.ncbi.nlm.nih.gov/Web/Newsltr/Spring04/blastlab.html ...
written 14 days ago by microfuge720
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Comment: C: Checking the quality and reliability in bioinformatics
... Would like to mention about git-lfs for large file (bams, vcfs ...) which are very typical of bioinformatics pipelines and can not be handled by usual git (https://git-lfs.github.com/) . Applies more for analysis rather than software development. ...
written 6 weeks ago by microfuge720
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Comment: C: Solvent- Accessible Surface Area
... Biopython module for DSSP seems to do that http://biopython.org/DIST/docs/api/Bio.PDB.DSSP%27-module.html ...
written 6 weeks ago by microfuge720
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Comment: C: which one is good mafft or clustalW???
... Page 44 of t-coffee pdf [here][1] provides a detailed comparison. [1]: https://media.readthedocs.org/pdf/tcoffee/latest/tcoffee.pdf ...
written 3 months ago by microfuge720
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Comment: C: Finding sample swaps using VCF files
... Hi, One quick way but not for a serious clinical settings is to feed the vcf to vcfkit ([here][1] ) and make a tree out of it. But I don't exactly know the implications for your work. We gave students of our course some paternity testing exercises based on SNPs and they came up with the idea to mak ...
written 3 months ago by microfuge720
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Comment: C: Retrieval of similar positions from samples in a vcf but different from referenc
... Would bcftools view work if min alternate allele frequency is set to 1.0 ? bcftools view --min-af 1 input.vcf.gz ...
written 3 months ago by microfuge720
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Comment: C: Assumed rate of exonic mutation?
... Not fully sure but the mutation rate should not be less in exons (assuming no DNA composition bias). It is the selection on exons which purges more mutations giving less polymorphism/divergence. Effects of linked selection would also effect synonymous sites decreasing polymorphism and divergence in ...
written 3 months ago by microfuge720
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Comment: C: Finding paralogs of gene
... I have used these two and find them to be good http://inparanoid.sbc.su.se/cgi-bin/index.cgi http://eggnogdb.embl.de/#/app/home ...
written 3 months ago by microfuge720
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Comment: C: size (how many amino acids) are cytosolic or extracellular in membrane protein
... Would [this][1] be of any use? never used it myself though. [1]: http://embnet.vital-it.ch/software/tmbase/TMBASE_doc.html ...
written 3 months ago by microfuge720
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Answer: C: How to print two lines of several files to a new file with the speicific order?
... Just a paste and awk based approach based on the assumption that a) the sequence is in one line and not wrapped b) no tabs spaces in parent fasta. The getline function in awk gets the next line and it is then skipped by awk. paste -d "\t" *.fa |awk '{getline y;split(y,z,"\t");for (i=1;i<=NF ...
written 3 months ago by microfuge720

Latest awards to microfuge

Scholar 3 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 3 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 4 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 4 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 4 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Supporter 13 months ago, voted at least 25 times.
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Centurion 13 months ago, created 100 posts.
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Scholar 15 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

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