Sansrity Sinha

11 Questions 60 Answers 0 Followers

Questions related from Sansrity Sinha

Does anyone know about tools that predict ancestral sequence for a phylogenetic tree?

I am looking for a tool that could predict the ancestral sequence for the phylogenetic tree. I have heard about FastML and MEGA6.0. Can anyone help me understand what do the alphabets M, L etc at...

17 December 2016 9,424 2 View

Is it possible to express and purify proteins in large quantities from mammalian cell lines ?

generally bacteria is used for protein expression in purification whenever protein is required in large quantities for structural studies. Is it possible to get such large amounts of proteins from...

13 August 2016 520 6 View

What is the general cut off used in CD-HIT when using a data set of closely related sequences for phyognetic analyses?

my dataset consists of highly similar sequences of proteins. i only wanted to remove duplicate sequeces if any in the data set. what threshold shall I set in CD HIT?

03 April 2016 4,539 1 View

Is Rev, vpx required for retroviral mediated transduction and overexpression of shRNA?

i wanted to create a stable knock don cell line for my gene of interest. i chose 3'UTR targetting shRNA cloned in a retroviral vector for that purpose. I am using pSuper as entry vector and pUMVC...

01 March 2016 9,098 0 View

What is the approximate length of amino acids that can be deleted from a protein using quick change method?

i wanted to delete a strech of 120 amino acids present between N and C terminal of my protein. is i possible to remove such a long stretch by quick change method? any specific consideration for...

26 August 2015 3,195 4 View

How does one annotate homologs and orthologs of gene of interest?

I am working on a protein family that has two members. I tried to look up homologs and orthologs in lower organisms. i found two hits for search indicating presence of both genes in lower...

08 August 2015 1,624 9 View

Can someone help with plasmid insert release problems when cloning?

hi, i have been trying to clone a fragment into pGEX6P1 vector. every time i amplify the insert (1.5kb), digested it with BamH1 and XhoI (sites flanking the insert), digest the vector too (since...

30 July 2015 4,421 3 View

Does a difference in the number of charged residues amongst two genes (one duplicated from the other) indicate any functional differences?

i am working on two proteins each translated from two different genes belonging to same gene family. A closer look at the sequence tells me that the proteins differ in the number of charged...

30 July 2015 7,676 4 View

How does one select the best fit model for constructing phylogenetic trees?

I am working on mitofusins which are of two types in humans (not isofoms, but two different genes encoding them). i want to know at what time in evolution did the duplication happen. also which...

18 June 2015 5,268 5 View

How can I optimize antibiotic concentrations for generating a gene of interest expressing stable cell line?

I have my gene of interest cloned in mammalian expression system. there are two gene that i am looking for. i have cloned each of them in two different plasmids both having different promotors of...

10 June 2015 9,616 3 View

Why does glycogen biosynthesis require UDP moiety in glycosyl transferase and not ADP?

although ADP is abundant in the cell and most reactions require ADP? does that has and additional evolutionary significance?

30 April 2015 9,976 3 View