User: ALchEmiXt

gravatar for ALchEmiXt
ALchEmiXt1.8k
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Location:
The Netherlands
Website:
http://www.wur.nl/biov...
Twitter:
a_bossers
Scholar ID:
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Last seen:
4 months ago
Joined:
6 years, 4 months ago
Email:
a***********@wur.nl

Working mainly on multi-Omics approaches using all kinds of OMICS tools, metagenomics, meta-transcriptomics, NGS and bioinformatics.
Linux enthousiast. Preferred languages/platforms: Perl, R, PHP, BASH, Ubuntu, galaxy
Occasionally you can find me on Twitter as well.
CU,
Alex

Posts by ALchEmiXt

<prev • 217 results • page 1 of 22 • next >
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Answer: A: Can we assembly the draft sequences that is assembled by another genome assemble
... Alternative is to provide SPAdes with so-called trusted contigs of your ABySS assembly. It sometimes can be beneficial to combine assemblies from different assembly strategies. If you have multiple sequencing rounds/technologies and *de novo* assemblies you could also try to merge those assemblies ...
written 8 months ago by ALchEmiXt1.8k
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Answer: A: phylip format from Mummer
... First thing you have to do is to convert the pair-wise MUMmer output into a distance metric. I have very good experience with the MUMi distance (as explained in [this paper][1]). Using that distance between pairwise alignments you can build a distance matrix on which you can perform for instance the ...
written 8 months ago by ALchEmiXt1.8k
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Comment: C: How to calculate the mass of whole protiens and sub regions?
... For MW calculations in automated setting I can recommend the EMBOSS suite of tools. ...
written 8 months ago by ALchEmiXt1.8k
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Answer: A: Metagenome/metatranscriptome db with blast option?
... If you have full metagenomic data (so not only 16S-amplicon barcoding as mentioned above) you could give metaphlan2 a try. We have good experience with their taxa specific reference database. It has to be run locally though: https://bitbucket.org/biobakery/metaphlan2 ...
written 8 months ago by ALchEmiXt1.8k
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Comment: C: How can a MSA be useful for sub-cellular location identification?
... ok. Then the MSA might help you using those domains to predict which region of you protein might be located intracellular, in memberane or exposed.... this annotation has to be known though for the ortologous domains. Alternatively use some of the subcellular localization tools out there. ...
written 8 months ago by ALchEmiXt1.8k
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Answer: A: How can a MSA be useful for sub-cellular location identification?
... I think what they mean is looking for orthologs or orthologous domains for which pdb templates could be available. You could use those domains for homology modelling... The MSA will help you to identify those regions of interest. ...
written 8 months ago by ALchEmiXt1.8k
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Comment: C: localhost doesn't work
... ok great. You updated or pulled a new version? Please accept the answer as solved. ...
written 8 months ago by ALchEmiXt1.8k
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Answer: A: localhost doesn't work
... For the last part of your question: Did you add the galaxy repository to your ubuntu repositories? Else the apt-get will not work. Follow the instructions on getgalaxy.org and you should be fine. However, isn't biolinux preconfigured to run galaxy? Then you should browse the biolinux website. Regu ...
written 8 months ago by ALchEmiXt1.8k
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Answer: A: Pairwise sequence alignment
... MUMmer is fast and fit for purpose. http://mummer.sourceforge.net/ ...
written 8 months ago by ALchEmiXt1.8k
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Answer: A: Data bases with proteins and ligands
... If protein to chemical interactions are also of interest checkout STITCH at http://stitch.embl.de/ Else checkout the resources at EBI like http://www.ebi.ac.uk/intact/ ...
written 8 months ago by ALchEmiXt1.8k

Latest awards to ALchEmiXt

Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Best Way To Close Gaps In Genome With Single Reads
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Add sequence lengths to headers in a fasta file
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Best Way To Close Gaps In Genome With Single Reads
Popular Question 15 months ago, created a question with more than 1,000 views. For Contaminant Filtering Large Fastq Data Sets
Popular Question 17 months ago, created a question with more than 1,000 views. For Contaminant Filtering Large Fastq Data Sets
Voter 17 months ago, voted more than 100 times.
Good Answer 21 months ago, created an answer that was upvoted at least 5 times. For A: How To Draw Genome Features Along Chromosome
Great Question 21 months ago, created a question with more than 5,000 views. For Contaminant Filtering Large Fastq Data Sets
Scholar 2.1 years ago, created an answer that has been accepted. For A: Average coverage of de novo SPAdes assembly deviates a lot from theretical cover
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Contaminant Filtering Large Fastq Data Sets
Good Question 2.6 years ago, asked a question that was upvoted at least 5 times. For Contaminant Filtering Large Fastq Data Sets
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Contaminant Filtering Large Fastq Data Sets
Popular Question 2.9 years ago, created a question with more than 1,000 views. For How Common Are Multi-Line Fastq Files?
Autobiographer 4.0 years ago, has more than 80 characters in the information field of the user's profile.
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Centurion 4.0 years ago, created 100 posts.
Guru 4.0 years ago, received more than 100 upvotes.
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Best Way To Close Gaps In Genome With Single Reads
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: Best Way To Close Gaps In Genome With Single Reads
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: Mapping Reads Back To Assembly Contigs
Teacher 5.7 years ago, created an answer with at least 3 up-votes. For A: How To Draw Genome Features Along Chromosome

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