User: microfuge

gravatar for microfuge
microfuge740
Reputation:
740
Status:
Trusted
Location:
Twitter:
@microfuge
Last seen:
an hour ago
Joined:
4 years, 11 months ago
Email:
s***********@gmail.com

Posts by microfuge

<prev • 166 results • page 1 of 17 • next >
0
votes
0
answers
138
views
0
answers
NCBI bacterial Morphology, environment and temperate data
... Hello, I remember that a long time back data about bacterial morphology, environment and growth temperate (thermophile or mesophile) used to be available from NCBI genomes ftp site. The [site][1] is also mentioned in the methods section of one of the papers [papers][2] . This data is still availab ...
ncbi ncbiftp written 12 weeks ago by microfuge740 • updated 6 weeks ago by Biostar ♦♦ 20
1
vote
1
answer
324
views
1
answers
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 5 months ago by microfuge740
0
votes
5
answers
516
views
5
answers
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 months ago by microfuge740
0
votes
0
answers
366
views
0
answers
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 months ago by microfuge740
1
vote
2
answers
855
views
2
answers
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 8 months ago by microfuge740
1
vote
0
answers
428
views
0
answers
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 8 months ago by microfuge740
1
vote
1
answer
387
views
1
answers
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 8 months ago by microfuge740
1
vote
0
answers
345
views
0
answers
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 8 months ago by microfuge740
2
votes
0
answers
547
views
0
answers
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 8 months ago by microfuge740
0
votes
0
answers
374
views
0
answers
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 8 months ago by microfuge740

Latest awards to microfuge

Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Popular Question 3 months ago, created a question with more than 1,000 views. For Tissue Specificity index (tau) should FPKM data be log transformed?
Scholar 8 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 8 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 9 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 9 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 9 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Commentator 18 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Supporter 18 months ago, voted at least 25 times.
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Centurion 18 months ago, created 100 posts.
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1049 users visited in the last hour