Pairwise alignment of DNA from a gene to coding RNA?

More Miguel Andrade's questions See All

How to find the mean, SD and CI in SPSS?

Hi, I hope that someone can help me with this task: I have 5 groups of participants which are numbered in SPSS from 1 to 5 (according to their group number) and are all under the variable group....

03 March 2021 506 3 View

Do you know any MR image dataset?

I would like to research on MR images (0.5T and 3T). Can you please suggest some websites that I can download dataset including both 0.5T and 3T MR images? Thank you.

02 March 2021 7,735 3 View

What pH condition required to coat APTES on silica coated Fe3O4?

It's a hydrolysis reaction, which may produce by either acid or base-catalyzed reaction. so can anybody help me with this, which condition is suitable for this reaction?

26 February 2021 1,760 8 View

What software programs can directly simulate Additive Manufacturing Directed Energy Deposition (DED)?

I understand there are a lot of software programs that can simulate DED by going through specific modeling, simulation, and commands. For me, that was time consuming and results were not accurate....

24 February 2021 4,428 3 View

What condition required for coating of Fe3O4@SiO2 by using APTES?

I tried coating Fe3O4@ SiO2 by using APTES in 5% water-ethanol but it is not coated. Kindly suggest a solution for it. Thanks

24 February 2021 5,992 4 View

How can I prevent bubbles from forming under a coverslip?

My colleague and I are having some trouble mounting 70 micrometer mouse brain slices. When we initially position the coverslip over the mounted slices, there are no bubbles but when we come back...

10 February 2021 3,580 1 View

What recipe of homemade lenti-virus concentrator do you use?

My lab is using a lenti-X concentrator. And we are looking for a homemade recipe. I have tried this recipe....

08 February 2021 5,965 1 View

What is the best visualisation solvent for xylooligosaccharides using TLC?

I am interested in using TLC to detect non-linear xylooligosaccharides. What would be the best visualisation solvent? Would aniline phthalate solution be suitable? I have also seen people...

02 February 2021 7,748 3 View

Photoelectrocatalysis: How to control exponential increase in cathodic wave during photoelectro/electrocatalysis?

We are trying to develop a reaction methodology using photoelectrocatalysis.While, we are giving a negative potential of -1.8V, on photoexcitation rise in cathodic wave is observed. What can be...

31 January 2021 5,239 3 View

Is there an open source tool the measures the GRAVY index of a peptide incorporating the PTMs and unusual amino acids (e.g. hydroxyproline)?

Right now, I am using ProtParam to compute GRAVY index of peptides. However, some of my peptides are post-translationally modified, and contains unusual amino acids. I assume that ProtParam does...

29 January 2021 8,300 4 View

Have someone successfully used the ER alpha (Santa Cruz sc-8002) antibody in immunostaining ?

Santa Cruz now recommends this new antibody (F-10) but I can't find a publication using this reference. I'm working on human et non human primate hypothalamus and so far, it doesn't work. Is...

02 March 2021 10,003 2 View

Gel electrophoresis result for total RNA samples, 1.5 Agarose gel was used, How to improve the integrity of RNA?

Gel electrophoresis, RNA degradation, RNA extraction from fresh tissue

02 March 2021 5,433 5 View

Problem with shRNA transfection. Why are only two plates getting contaminated instead of all?

I transfected my LNCaP-WT cells with 3 shRNA plus their NTC two weeks ago and split two puromycin selected cell plates on Friday last week(Feb 26). I checked for GFP in the cells, and they all...

28 February 2021 4,949 3 View

Does anyone use antinuclear antibody (ANA) and anti-Phospholipid antibody ELISA kit for Non Human Primate serum samples?

I am looking for anti-nuclear antibody (ANA) and anti-Phospholipid antibody ELISA kit for Non Human Primate serum samples. Any suggestions highly appreciated. Thank you.

28 February 2021 6,512 3 View

Any specific pipeline or parameter to analyse total transcriptomics study of brain tissue samples?

I have two groups of brain samples, control and treated for example. It was total RNA nova seq sequencing. I tried all the available pipeline like: star+rsem+deseq2, Hista+stringtie+cuffdiff,...

27 February 2021 356 6 View

Why is the efficiency of viral mRNA electroporation in PBMC low?

Hello, I have been struggling with the electroporation of PBMC with HIV-I mRNA. Although the quality of the RNA generated is good, and the handling of the cells in meticulous, the frequency of...

27 February 2021 9,233 3 View

What is the best concentration of cDNA to be used for qPCR?

I have synthesised cDNA from 500ng/ul of RNA. The concentration of the cDNA Is about 5000ng/ul. Should I dilute my cDNA or just use it as it is for my qPCR? I usually use 2ul of cDNA for a 20ul...

24 February 2021 8,618 3 View

Recommendations on homogenizers for RNA isolation?

I will be performing RNA isolation with frozen lung biopsy samples and am in the market for a tissue homogenizer. I am wanting a homogenizer that will fit in a 1.5ml tube. I was looking at the...

24 February 2021 3,623 3 View

RNA-seq DEGs downstream analysis and reporting in literature?

I used EdgeR to get the list of DEGs (differentially expressed genes) from my liver RNA-seq experiment. I have done the gene overrepresentation and GSEA based pathway analysis. I am currently...

23 February 2021 8,969 1 View

Is it efficient to do liquid biopsy to investigate the gene expressions of the tumor?

To do liquid biopsy and look for specific gene expressions there are so many published papers. Thera are different protocols and procedures used to isolate circulating cell free RNA or mRNA from...

23 February 2021 7,326 5 View

Albino Bacolla

I would use blast from NCBI (https://blast.ncbi.nlm.nih.gov/Blast.cgi) on a database of cDNAs. However, if I were interested in the protein product I would use protein sequences and not cDNAs because the latter tend to be more divergent than the former.

Frederic Lepretre

Hi Miguel,

you can also use the blast from the UCSC (http://genome.ucsc.edu/cgi-bin/hgBlat) where in addition to the data you'll have a useful genome browser with lot of optional tracks (you can apply your own custom track also).

fred

For multiple alignments see if Clustal Omega (https://www.ebi.ac.uk/Tools/msa/clustalo/) may be useful to you.