User: dago

gravatar for dago
dago2.1k
Reputation:
2,060
Status:
Trusted
Location:
Germany
Last seen:
19 hours ago
Joined:
2 years, 10 months ago
Email:
s***********@gmail.com

Posts by dago

<prev • 386 results • page 1 of 39 • next >
0
votes
0
answers
84
views
0
answers
Comment: C: Align multiple gene clusters: mummer skips random sequences in multi fasta files
... Well, my input data are indeed portion of genomes, and I want to find maximal matches amongst them. So for me it sounds quite good. ...
written 16 days ago by dago2.1k
0
votes
0
answers
84
views
0
answers
Comment: C: Align multiple gene clusters: mummer skips random sequences in multi fasta files
... Thanks for the answer. Why do you think so? ...
written 16 days ago by dago2.1k
0
votes
0
answers
84
views
0
answers
Align multiple gene clusters: mummer skips random sequences in multi fasta files
... I have a multi fasta containing 100s of gene clusters. I would like to align them and calculate a % identity. I tried to use mummer, using the same multi fasta as both query and reference. At first I thought that it worked really well, but then I saw something odd. There are two clusters in the mul ...
gene alignment sequence genome written 17 days ago by dago2.1k
30
votes
2
answers
830
views
23 follow
2
answers
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 12 weeks ago by dago2.1k
4
votes
1
answer
231
views
1
answers
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 4 months ago by dago2.1k
0
votes
1
answer
225
views
1
answers
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 4 months ago by dago2.1k
0
votes
1
answer
220
views
1
answers
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 4 months ago by dago2.1k
0
votes
1
answer
216
views
1
answers
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 4 months ago by dago2.1k
0
votes
2
answers
233
views
2
answers
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 4 months ago by dago2.1k
2
votes
1
answer
195
views
1
answers
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 4 months ago by dago2.1k

Latest awards to dago

Popular Question 25 days ago, created a question with more than 1,000 views. For Map gene gain and loss in phylogenetic tree
Popular Question 27 days ago, created a question with more than 1,000 views. For Map gene gain and loss in phylogenetic tree
Student 8 weeks ago, asked a question with at least 3 up-votes. For Map gene gain and loss in phylogenetic tree
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Map gene gain and loss in phylogenetic tree
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Map gene gain and loss in phylogenetic tree
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: scatter plot tool
Popular Question 3 months ago, created a question with more than 1,000 views. For Cluster proteins according to their domain architecture
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: scatter plot tool
Scholar 4 months ago, created an answer that has been accepted. For A: GO enrichment analysis using non model organism
Popular Question 4 months ago, created a question with more than 1,000 views. For Cluster proteins according to their domain architecture
Scholar 4 months ago, created an answer that has been accepted. For A: GO enrichment analysis using non model organism
Scholar 4 months ago, created an answer that has been accepted. For A: GO enrichment analysis using non model organism
Librarian 4 months ago, created a post with more than 10 bookmarks. For Learning Python: list of resources
Prophet 4 months ago, created a post with more than 20 followers. For Learning Python: list of resources
Popular Question 5 months 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 5 months ago, created a post with more than 5 votes. For A: What Do You Waste Your Time On
Popular Question 5 months ago, created a question with more than 1,000 views. For Associate to GO Names the respective IDs
Scholar 6 months ago, created an answer that has been accepted. For A: GO enrichment analysis using non model organism
Scholar 6 months ago, created an answer that has been accepted. For A: GO enrichment analysis using non model organism
Popular Question 7 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 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 8 months ago, created a question with more than 1,000 views. For Reduce redundancy in a GO enrichment analysis
Popular Question 9 months ago, created a question with more than 1,000 views. For Reduce redundancy in a GO enrichment analysis
Popular Question 11 months ago, created a question with more than 1,000 views. For What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2014?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1494 users visited in the last hour