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Questions related from Stefano Campanaro
We are hiring! Are you a postdoc or did you just graduate? Would you like to work on metabolics flux balance or microbial genomics for anaerobic digestion topic? Then contact us! We are looking...
08 August 2019 1,985 3 View
Next year I will start teaching metagenomics to master students (mainly focused on bioinformatics). Can anyone recommend a text book related to this topic? I am also interested in other related...
06 June 2019 1,437 16 View
Hi, I would like to perform gene disruption in Lactobacillus paracasei. Could you provide a protocol or suggest a grup which is able to perform this kind of analysis? Thank you
08 August 2018 4,435 1 View
I am checking different methods to perform hierarchical clustering with a very large number of elements (between 100,000 and 500,000). I have tried many different software like MeV, Cluster, etc....
11 November 2015 7,638 4 View
I am comparing a large number of microbial genomes obtained from a complex microbial community. I performed the main functional annotations for the genes (COG, KEGG, Pfam) and I would perform a...
02 February 2015 9,970 1 View
We are planning a metatranscriptomic analysis on a microbial community obtained from bioreactors, but we need to remove as much rRNA as possible in order to maximize the number of reads on mRNA....
06 June 2014 3,732 5 View
We are performing trial shotgun assemblies of 80 millions paired-end sequences illumina reads obtained from a bioreactor microbial community. After removing contigs shorter than 1kbp, the assembly...
04 April 2014 7,449 1 View
I am planning analysis on a complex microbial community containing high number of species of bacteria and archaea using 16 rDNA sequencing. On previous experiments I have used two different...
02 February 2014 8,835 8 View
I am trying to align short reads DNA sequences on a reference database comprising all the prokaryotic genomes reported at the ncbi. Unfortunately I noticed that both BOWTIE and BWA have a maximum...
12 December 2013 4,583 4 View
Does someone have assembled short reads obtained from shotgun sequencing (Proton sequencer) of complex microbial communities? Which is the best tool for assembly of these reads (not-paired-end)?...
09 September 2013 7,025 4 View
I am analyzing a bacterial genome recently sequenced in our group. After gene finding and annotation I would have a rough overview of its operon structure using a bioinformatic software. Can...
09 September 2013 3,600 1 View
I am using STAMP software to analyze 16S metagenomic data. Basically I have two experimental replicates for six different experiments. The first three experiments were performed in a specific...
07 July 2013 3,176 4 View
I am looking for a simple method (or software) to identify ORI in plasmid sequence of some Lactobacillus species. Some of the plasmids are very large and cannot be analyzed using software like...
06 June 2013 5,713 1 View
I am assembling Illumina sequences (MySEQ paired end 250+250 bases) obtained for bacterial genomes. I used both Velvet and Abyss software but I did not obtained a quality files for the genome...
06 June 2013 4,094 7 View
I'm starting a metagenomic analysis on an environmental microbial community (bacteria and eukaryotes). My aim is to characterize the community at the genus or species level. Is it better to...
04 April 2013 1,655 21 View
