User: dago

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dago2.1k
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Posts by dago

<prev • 390 results • page 1 of 39 • next >
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Answer: A: Identifying core proteins -Pangenome
... I am not familiar with the program you are using. But if the result of the analysis are contigs, I guess as a product of a whole genome alignment, I would say that in 99.9% of the case you will have multiple genes on them. Therefore you would need to do 2 things: gene calling and annotation(if neede ...
written 8 days ago by dago2.1k
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Comment: C: Bacterial de novo genome assembly
... Look these: https://www.biostars.org/p/120386/ And also a list of tools available is [here][1]. You can check the one that work in windows amongst them. [1]: https://omictools.com/genome-assembly-category ...
written 20 days ago by dago2.1k
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Comment: C: Bacterial de novo genome assembly
... check assembly quality with [QUAST][1] [1]: http://bioinf.spbau.ru/quast ...
written 24 days ago by dago2.1k
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Comment: C: De novo genome assembly
... what did you try? There are plenty of tutorials out there. What organism do you have? Bacteria? ...
written 25 days ago by dago2.1k
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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 10 weeks ago by dago2.1k
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Comment: C: Align multiple gene clusters: mummer skips random sequences in multi fasta files
... Thanks for the answer. Why do you think so? ...
written 10 weeks ago by dago2.1k
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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 10 weeks ago by dago2.1k
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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 4 months ago by dago2.1k
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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 5 months ago by dago2.1k
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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 5 months ago by dago2.1k

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Popular Question 16 hours ago, created a question with more than 1,000 views. For Cluster proteins according to their domain architecture
Popular Question 20 days ago, created a question with more than 1,000 views. For Map gene gain and loss in phylogenetic tree
Scholar 23 days ago, created an answer that has been accepted. For A: GO enrichment analysis using non model organism
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Map gene gain and loss in phylogenetic tree
Great Question 6 weeks ago, created a question with more than 5,000 views. For Available pipelines for functional annotaiton (COG, KEGG, GO) of genomes
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Map gene gain and loss in phylogenetic tree
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Map gene gain and loss in phylogenetic tree
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Map gene gain and loss in phylogenetic tree
Student 3 months ago, asked a question with at least 3 up-votes. For Map gene gain and loss in phylogenetic tree
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Popular Question 4 months ago, created a question with more than 1,000 views. For Map gene gain and loss in phylogenetic tree
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Popular Question 5 months ago, created a question with more than 1,000 views. For Cluster proteins according to their domain architecture
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