Johnny Tam

7 Questions 2 Answers 0 Followers

Questions related from Johnny Tam

What is the standard way of preparing homolog sequences for a phylogenetic analysis?

I have two protein sequences with around 50% identity between them. I want to study the phylogenetic relationship between them. I came up with a method myself: Step 1: blast each of the sequences...

12 November 2018 3,717 2 View

Pull-down of transcription factors from cell lysate using biotinylated DNA probe?

I want to pull the transcription factors which binds to the biotinylated DNA probe of promoter sequence flanked 5' of a gene of interest. Any technical advice on the following questions? Probe...

18 February 2018 3,759 5 View

Suggestion on contig assembler which respect a single copy mutation in a nonaploid genome?

As title, and the following is the background FYI : I am discovering a possible single copy insertional mutation in a nonaploid plant genome. Previously I used SPades to assemble contigs of the...

23 October 2017 3,685 0 View

Is there any read-mapping package that could map only the first half or the second half of reads?

I have a 150bp short read whole-genome library by analyzing which I am trying to discover the breakpoint of a possible insertional mutation in a plant genome. I am wondering Is there any...

17 October 2017 7,522 2 View

What are the principles of controlling bioinformatics procedures and balancing between screening efficiency and the risk of losing a real candidate?

I am trying to identify the point of insertion in the genome that may have caused the size difference in fruits between wild-type and mutant of a plant species (also mentioned here :...

14 October 2017 2,267 1 View

Getting isolated bands from restriction cutting a large plant genome (>800Mbp). Any good idea?

I am trying to get isolated bands from restriction digestion of a large plant genome (>800Mbp). After discussing with the people in my lab, their experience seems to have got a smear instead of...

12 September 2017 7,345 4 View

Working Principle of Ancestral Sequence Reconstruction (ASR)

Hi, I am now trying to work on the ancestral sequence reconstruction of a protein of interest. I am trying to understand the working principle and have looked into related topics such as parsimony...

01 January 1970 2,440 0 View