Which program is good for finding the core genome and singleton genes of mulitple chloroplast genomes?

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...

06 July 2016 2,163 2 View

How to do PCR using highly degraded DNA as templates?

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....

06 July 2016 2,899 5 View

Can transcriptional elongation factor 1 alpha (tef) be used as a phylogenetic marker for protists and metazoa?

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...

01 February 2016 3,816 2 View

Is univariate or multivariate analysis most suitable for my data?

11 December 2015 5,403 4 View

Does anyone happen to have the script that can convert blast output against Swissprot to GO terms?

http://enveomics.blogspot.com/2012/11/semantics.html As showed above, this is a collection of handy scripts but haven't been deposited in github. I tried to find the dropbox download link but I...

07 August 2015 8,683 3 View

Where to find the output of kmernorm?

04 May 2015 9,150 0 View

Is RNA-seq reads number related to the quality of RNA preparation?

Dear all, I don't have much experience of RNA-seq. I noticed that the reads number of one treatment (3 individuals) was lower than the other treatment. Similarly, the signal intensity of samples...

04 May 2015 3,222 9 View

Why 16S rRNA gene can't be found in my single-cell genome assembly ?

01 February 2015 2,428 11 View

Which genes are responsible for fungal hyphae development?

01 February 2015 6,048 5 View

Would horizontal gene transfer happen on house-keeping/ultraconservative genes?

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...

31 December 2014 3,553 7 View

How to normalise data on OPM package from R Studio ?

Good afternoon, I recently used OmniLog from BIOLOG for my experimentations : I tested the metabolism of different strains on 2 types of plates. I have 16 strains of 3 different groups...

02 March 2021 3,584 1 View

Where to find data on trees in tropical agroforestry?

Hi, I'm looking for data (mainly related to management: growth rate, canopy size, soil and climate preferences, etc.) about tropical trees used in tropical agroforestry. Have you ever heard about...

28 February 2021 7,356 8 View

The Shannon's index is inversely proportional to Simpson's index (1-D)?

I'm having a problem with my bloxplot with Shannon's and Simpson's indexs. The value of Shannon for my Community 1 indicating higher diversity (in relation of the Community 2), but have lower...

26 February 2021 3,033 9 View

Has anyone used the Illumina ITS1 primer sets?

Hi everyone, Illumina provides a list of primers to amplify with high taxonomic coverage the ITS1 region for further fungal sequencing, but I cannot find the exact amount necessary of each...

25 February 2021 6,969 3 View

Is there any one who can provide a donation of HPV detection and genotyping kits in exchange collaboration fors?

Warm greetings My name is Ayichew S. and I am doing my Ph.D. in Medical Microbiology (on Human papillomavirus). At this stage, I have almost completed a clinical sample Cervical swabs)...

25 February 2021 1,660 3 View

Is there any one who can provide a donation of HPV detection and genotyping kits in exchange collaboration forms?

Warm greetings! My name is Ayichew S. and I am doing my Ph.D. in Medical Microbiology focusing on Human papillomavirus). At this stage, I have almost completed a clinical sample (Cervical swabs)...

25 February 2021 3,612 3 View

Advice on growing lactobacillus species in the lab?

Hello everyone, For part of my PhD project, I'm hoping to grow some lactobacillus species in the lab so that I can create standard curves for a qPCR quantification of a faecal sample. However, I...

24 February 2021 3,157 6 View

Where can I find raw quantitative datasets on ecosystem services?

I'm an Undergraduate student on the search for a research topic which has to involve any ecosystem service(s) and a response to environmental change. I'm looking for raw quantitative data sets (I...

19 February 2021 5,911 2 View

Any recommendations for methods to analyze elephant space-use (using GPS) and correlating this with changes in NDVI?

For my Masters I am looking into elephant space-use and its effect on vegetation change. I have elephant GPS collar data and was going to use Google Earth Engine to obtain NDVI values. I would...

16 February 2021 7,097 3 View

How to consider effects of rapid warm adaptation in modeling of ecological impacts of warming?

I would highly appreciate it if my fellow ecologists (biologists) provide their opinion on the thoughts below [esp., shortly tell us which path may be more effective, if they know another way, if...

15 February 2021 3,642 6 View