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Questions related from Fang Liu
Dear all, I am interested in finding the core genome and singleton genes from a dataset of multiple chloroplast genomes (n=12). I don't have much experience in bidirectional BLAST. Can anyone...
11 July 2016 7,462 2 View
Dear all, One of my friends has to amplify some species-specific genes from cooking oil, which contained little and mostly degraded DNA. I think paleontologists often work on degraded ancient DNA....
08 July 2016 8,140 4 View
Dear all, One of my friends is working on the detection of species-specific DNA sequences in plant oil (to find out the potential adulteration) and ask me for advice, e.g. probe design. Their plan...
08 July 2016 7,760 12 View
Dear all, I study marine sponges and their symbiotic microbes. I have some RNA-seq data of sponge transcriptomes. I wonder if there's any gene that can indicate the metabolic/respiratory rate of...
21 May 2016 4,819 1 View
Dear all, I've found highly diverse and actively expressed genes related to aromatic carboxylic acids degradation from sponge-associated microbes. However I am not aware of the sources of...
11 May 2016 7,545 7 View
Hello, I know tef can be used as a phylogenetic marker for fungi. But what about other organisms? For eukaryotes, 18S rRNA is definitely too conservative in many cases. By the way, COI is used in...
22 February 2016 548 2 View
Hey guys,I just started using Cufflinks on Galaxy (2.2.1) to analysis my RNA-seq data. But the tutorial example I found was quite simple (2 samples comparison) and I got a bit confused. I have the...
26 July 2015 9,577 4 View
Dear all, I recently got some viral assemblies from sponge metagenome. As for bacteria, people use essential gene counting to evaluate the completeness of an assembly. But how to evaluate the...
22 April 2015 8,433 2 View
Hi guys, this is my first time to use Trinity. I used lsf to submit my task to a remote sever. It's has been almost 48hours yet trinity is still in '[bam_sort_core] merging from 13 files...'. I...
05 March 2015 4,552 3 View
Dear all, In my previous question (https://www.researchgate.net/post/Why_16S_rRNA_gene_cant_be_found_in_my_single-cell_genome_assembly#54ef76f7f15bc7a4138b4618), I was advised to assemble my SAGs...
27 February 2015 2,189 1 View
Hi all, I have no experience with CARD-FISH. But right now I suffered a lot from the autofluorescence of the sponges symbionts, which I tried to target. The autofluorescence was strong and...
05 February 2015 8,462 6 View
Hi guys, just a random question. As HGT frequently happen in microbial world, could house-keeping genes, e.g. gyrB, COI, rRNA be horizontally transferred between microbes? Any input is...
12 January 2015 1,513 6 View
Hi guys, I‘ve seen people who study coral micro-biome using coral mucus, coral tissues, and seawater over coral surface( within 1cm) . But which one is the best/most suitable? Why do people want...
17 December 2014 7,673 5 View
Hi guys, By analysing the microbial metagenomics, I found lots of genetic traits related to metal resistance and organic remediation, suggesting the water pollution in ambient seawater. I've heard...
25 November 2014 1,881 3 View
Hey guys, I am helping a coworker to build a fungal phylogenetic tree. In brief, the sequences were amplified by EF4/FUNG5 from ocean environmental DNA. Clone libraries were constructed and the...
24 July 2014 463 4 View
I want to know how corals can affect the pH and other nutrients concentration of ambient seawater? I overheard someone talking about how corals could lower down the ambient pH. But I don't know...
17 June 2014 4,374 9 View
One thing that keeps rolling in my head these days is the impact of HGT on microbial genetic diversity. I am not an expert in HGT so I can't really figure out some points. I started to get to know...
19 March 2014 1,371 1 View
I am processing a big dataset from functional microarry (Geochip 4.0). I somehow made the heatmap but I found there was no color bar to show the abundance variance across different samples. It...
31 January 2014 1,481 0 View
I am still new to some basic ecological concepts. I am dealing with a certain sponge which can grow on rock, coral reefs, and macro algae. Say, if I want to find out the factor that shapes the...
16 January 2014 3,838 2 View
I just downloaded an alignment of fungal EF1a from AFTOL (http://wasabi.lutzonilab.net/pub/alignments/download_alignments). But it's in nex format which I've never seen before. Now I want to...
02 December 2013 8,483 3 View
I am going to use D1-D2 domain for barcoding sponge-associated fungi. My primer choice is LR0R&LR3, generating 600bp products. But I didn't see any articles talking about the cutoff for 28S rRNA...
20 November 2013 8,278 2 View
I found in MEGA5, after bootstrap test, there was no scale bar in my bootstrap consensus tree. While in the original tree, there was a scale bar. Does anyone know why this happens in MEGA5?
26 October 2013 7,623 3 View
I am studying the active fungi in marine sponges. According to this paper...
24 September 2013 5,306 2 View
I am trying to detect the active eukaryotic microbes / protists from marine sponge transcripts. I think 18S rRNA can be detected as long as the cell is well preserved during sampling. Thus, only...
04 September 2013 4,266 4 View
