User: dago

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Posts by dago

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Forum: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2016?
... A new year just finished and many new exciting discoveries/programs/methods have been published. In consistency with previous Discussions https://www.biostars.org/p/128889/ https://www.biostars.org/p/15417/ https://www.biostars.org/p/4858/ https://www.biostars.org/p/171860/ What do you think ...
assembly forum rna-seq 2016 sequencing written 16 days ago by dago2.0k
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Answer: A: Troubleshooting interproscan standalone run
... The answer to your question is here: http://computing.bio.cam.ac.uk/local/doc/iprscan-faqs.html > InterProScan gives me a report file containing some errors from FingerPRINTScan that are weird like : ERROR: Calculation has exceeded maximum allowed complexity Fingerprint PRICHEXTENSN matches thi ...
written 7 weeks ago by dago2.0k
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Answer: A: Metagenomic shotgun sequence analysis- optimal approach
... I think it really depends on your specific questions. There could be really different approach to follow. For example, if you are interested in only specific genes then a binning would be not the ideal thing to do especially if you have complex samples as sediments or soil. You can start here: [Int ...
written 8 weeks ago by dago2.0k
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Answer: A: Antibiotic targets in bacteria
... You can type the name of the antibiotic [here][1] and you will get all sort of information on the molecules and mode of action. [1]: https://www.drugbank.ca/ ...
written 8 weeks ago by dago2.0k
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Answer: A: finding conserved regions of an allignment automaticallg by a software
... You can try [Gblock][1]. However, if your aim is to design primers that would be able to be as inclusive as possible I would suggest you to design degenerate primers. You can look [here][2] as a start. [1]: http://molevol.cmima.csic.es/castresana/Gblocks_server.html [2]: https://omictools.com/ ...
written 8 weeks ago by dago2.0k
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Answer: A: Predicting bacteria pathway based on whole genome sequence
... The easiest way is to blast the protiens against db as KEGG. YOu can use web tools like [BlastKOALA][1]. In the results then you can navigate amongst the different pathways identified. Of course this will require some manual curation to be sure that eventually missing enzyme are coded in the genome. ...
written 8 weeks ago by dago2.0k
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Answer: A: SignalP results - extract full sequence for proteins with a signal peptide
... take the ID of the proteins, for example: cat results_here | grep ">" > Ids_of_positive_proteins and then use `pyfaidx` as explained by https://www.biostars.org/u/1681/ here: https://www.biostars.org/p/126204/#126217 The original multifasta would be the file where you have the complet ...
written 9 weeks ago by dago2.0k
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Comment: C: Bacteria metabolites extraction protocol
... I am sorry but I do not think that this is the right forum for this type of question. ...
written 9 weeks ago by dago2.0k
0
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Answer: A: Check contamination in assembly
... These are some really good tools: [Metawatt][1] [CheckM][2] [(PHYL)AMPHORA][3] [1]: https://sourceforge.net/p/metawatt/wiki/Home/ [2]: http://ecogenomics.github.io/CheckM/ [3]: http://wolbachia.biology.virginia.edu/WuLab/Software.html ...
written 9 weeks ago by dago2.0k
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Answer: A: convert .fasta to .gft fomat
... Few links that might help: http://seqanswers.com/forums/showthread.php?t=44455 https://biostar.usegalaxy.org/p/1835/ http://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html ...
written 9 weeks ago by dago2.0k

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Popular Question 1 day ago, created a question with more than 1,000 views. For Map gene gain and loss in phylogenetic tree
Popular Question 5 days ago, created a question with more than 1,000 views. For Map gene gain and loss in phylogenetic tree
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: scatter plot tool
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Cluster proteins according to their domain architecture
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: scatter plot tool
Scholar 7 weeks ago, created an answer that has been accepted. For A: GO enrichment analysis using non model organism
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Cluster proteins according to their domain architecture
Scholar 9 weeks ago, created an answer that has been accepted. For A: GO enrichment analysis using non model organism
Scholar 10 weeks ago, created an answer that has been accepted. For A: GO enrichment analysis using non model organism
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Popular Question 11 weeks ago, created a question with more than 1,000 views. For Verify if all the components of a pathway are present in a genomes
Appreciated 12 weeks ago, created a post with more than 5 votes. For A: What Do You Waste Your Time On
Popular Question 3 months ago, created a question with more than 1,000 views. For Associate to GO Names the respective IDs
Scholar 3 months ago, created an answer that has been accepted. For A: GO enrichment analysis using non model organism
Scholar 3 months ago, created an answer that has been accepted. For A: GO enrichment analysis using non model organism
Popular Question 5 months ago, created a question with more than 1,000 views. For What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2014?
Popular Question 5 months ago, created a question with more than 1,000 views. For What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2014?
Popular Question 6 months ago, created a question with more than 1,000 views. For Reduce redundancy in a GO enrichment analysis
Popular Question 7 months ago, created a question with more than 1,000 views. For Reduce redundancy in a GO enrichment analysis
Popular Question 8 months ago, created a question with more than 1,000 views. For What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2014?
Popular Question 9 months ago, created a question with more than 1,000 views. For Associate to GO Names the respective IDs
Popular Question 9 months ago, created a question with more than 1,000 views. For Associate to GO Names the respective IDs
Scholar 9 months ago, created an answer that has been accepted. For A: GO enrichment analysis using non model organism

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